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Nikolay Dokholyan - Publications

Affiliations: 
1999 Boston University, Boston, MA, United States 
 2002- Biochemistry and Biophysics University of North Carolina, Chapel Hill, Chapel Hill, NC 
Area:
Molecular etiologies of human diseases
Website:
http://www.med.unc.edu/biochem/people/faculty/primary/dokholyan
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Year Citation  Score
2023 Lawanprasert A, Sloand JN, Vargas MG, Singh H, Eldor T, Miller MA, Pimcharoen S, Wang J, Leighow SM, Pritchard JR, Dokholyan NV, Medina SH. Deciphering the mechanistic basis for perfluoroalkyl-protein interactions. Chembiochem : a European Journal of Chemical Biology. e202300159. PMID 36943393 DOI: 10.1002/cbic.202300159  0.309
2022 Zhang DY, Wang J, Fleeman RM, Kuhn MK, Swulius MT, Proctor EA, Dokholyan NV. Monosialotetrahexosylganglioside Promotes Early Aβ42 Oligomer Formation and Maintenance. Acs Chemical Neuroscience. PMID 35713284 DOI: 10.1021/acschemneuro.2c00221  0.616
2021 Muralidharan A, Samoshkin A, Convertino M, Piltonen MH, Gris P, Wang J, Jiang C, Klares R, Linton A, Ji RR, Maixner W, Dokholyan NV, Mogil JS, Diatchenko L. Identification and characterization of novel candidate compounds targeting 6- and 7-transmembrane mu-opioid receptor isoforms. British Journal of Pharmacology. PMID 33782947 DOI: 10.1111/bph.15463  0.731
2020 Piltonen M, Krokhotin A, Parisien M, Bérubé P, Djambazian H, Sladek R, Dokholyan NV, Shabalina SA, Diatchenko L. Correction to: Alternative Splicing of Opioid Receptor Genes Shows a Conserved Pattern for 6TM Receptor Variants. Cellular and Molecular Neurobiology. PMID 33201419 DOI: 10.1007/s10571-020-00999-9  0.457
2020 Piltonen M, Krokhotin A, Parisien M, Bérubé P, Djambazian H, Sladek R, Dokholyan NV, Shabalina SA, Diatchenko L. Alternative Splicing of Opioid Receptor Genes Shows a Conserved Pattern for 6TM Receptor Variants. Cellular and Molecular Neurobiology. PMID 33010019 DOI: 10.1007/s10571-020-00971-7  0.475
2020 Wu HD, Kikuchi M, Dagliyan O, Aragaki AK, Nakamura H, Dokholyan NV, Umehara T, Inoue T. Rational design and implementation of a chemically inducible heterotrimerization system. Nature Methods. PMID 32747768 DOI: 10.1038/S41592-020-0913-X  0.72
2020 Miao Z, Adamiak RW, Antczak M, Boniecki MJ, Bujnicki JM, Chen SJ, Cheng CY, Cheng Y, Chou FC, Das R, Dokholyan NV, Ding F, Geniesse C, Jiang Y, Joshi A, et al. RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers. Rna (New York, N.Y.). PMID 32371455 DOI: 10.1261/Rna.075341.120  0.46
2019 Proctor EA, Mowrey DD, Dokholyan NV. β-Methylamino-L-alanine substitution of serine in SOD1 suggests a direct role in ALS etiology. Plos Computational Biology. 15: e1007225. PMID 31323035 DOI: 10.1371/Journal.Pcbi.1007225  0.642
2019 Zhu C, Han Q, Samoshkin A, Convertino M, Linton A, Faison EM, Ji RR, Diatchenko L, Dokholyan NV. Stabilization of μ-opioid receptor facilitates its cellular translocation and signaling. Proteins. PMID 31141214 DOI: 10.1002/Prot.25751  0.755
2019 Bonfanti S, Lionetti MC, Fumagalli MR, Chirasani VR, Tiana G, Dokholyan NV, Zapperi S, La Porta CAM. Molecular mechanisms of heterogeneous oligomerization of huntingtin proteins. Scientific Reports. 9: 7615. PMID 31110208 DOI: 10.1038/S41598-019-44151-0  0.557
2019 Dagliyan O, Dokholyan NV, Hahn KM. Engineering proteins for allosteric control by light or ligands. Nature Protocols. PMID 31076662 DOI: 10.1038/S41596-019-0165-3  0.78
2019 Dokholyan NV, Dagliyan O, Hahn KM. Control of Cellular Networks by Structural Disorder Biophysical Journal. 116: 490a. DOI: 10.1016/J.Bpj.2018.11.2645  0.722
2018 Dagliyan O, Krokhotin A, Ozkan-Dagliyan I, Deiters A, Der CJ, Hahn KM, Dokholyan NV. Computational design of chemogenetic and optogenetic split proteins. Nature Communications. 9: 4042. PMID 30279442 DOI: 10.1038/S41467-018-06531-4  0.777
2018 Luo J, Samanta S, Convertino M, Dokholyan NV, Deiters A. Reversible and Tunable Photoswitching of Protein Function through Genetic Encoding of Azobenzene Amino Acids in Mammalian Cells. Chembiochem : a European Journal of Chemical Biology. PMID 30277634 DOI: 10.1002/Cbic.201800226  0.721
2018 Han Q, Liu D, Convertino M, Wang Z, Jiang C, Kim YH, Luo X, Zhang X, Nackley A, Dokholyan NV, Ji RR. miRNA-711 Binds and Activates TRPA1 Extracellularly to Evoke Acute and Chronic Pruritus. Neuron. PMID 30033153 DOI: 10.1016/J.Neuron.2018.06.039  0.67
2018 Wang C, Aleksandrov AA, Yang Z, Forouhar F, Proctor EA, Kota P, An J, Kaplan A, Khazanov N, Boël G, Stockwell BR, Senderowitz H, Dokholyan NV, Riordan JR, Brouillette CG, et al. Ligand binding to a remote site thermodynamically corrects the F508del mutation in the human cystic fibrosis transmembrane conductance regulator. The Journal of Biological Chemistry. PMID 29903914 DOI: 10.1074/Jbc.Ra117.000819  0.781
2018 Luo J, Samanta S, Convertino M, Dokholyan NV, Deiters A. Front Cover: Reversible and Tunable Photoswitching of Protein Function through Genetic Encoding of Azobenzene Amino Acids in Mammalian Cells (ChemBioChem 20/2018) Chembiochem. 19: 2120-2120. DOI: 10.1002/Cbic.201800570  0.694
2017 Williams B, Zhao B, Tandon A, Ding F, Weeks KM, Zhang Q, Dokholyan NV. Structure modeling of RNA using sparse NMR constraints. Nucleic Acids Research. PMID 29165648 DOI: 10.1093/Nar/Gkx1058  0.473
2017 Williams B, Convertino M, Das J, Dokholyan NV. Molecular Mechanisms of the R61T Mutation in Apolipoprotein E4: A Dynamic Rescue. Biophysical Journal. PMID 28916386 DOI: 10.1016/J.Bpj.2017.08.026  0.742
2017 Dronamraju R, Ramachandran S, Jha DK, Adams AT, DiFiore JV, Parra MA, Dokholyan NV, Strahl BD. Redundant Functions for Nap1 and Chz1 in H2A.Z Deposition. Scientific Reports. 7: 10791. PMID 28883625 DOI: 10.1038/S41598-017-11003-8  0.449
2017 Brodie NI, Popov KI, Petrotchenko EV, Dokholyan NV, Borchers CH. Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations. Science Advances. 3: e1700479. PMID 28695211 DOI: 10.1126/sciadv.1700479  0.305
2017 Dagliyan O, Karginov AV, Yagishita S, Gale ME, Wang H, DerMardirossian C, Wells CM, Dokholyan NV, Kasai H, Hahn KM. Engineering Pak1 allosteric switches. Acs Synthetic Biology. PMID 28365983 DOI: 10.1021/Acssynbio.6B00359  0.743
2017 Khan A, Convertino M, Maixner W, Dokholyan N. (147) Structural basis underlying the interaction between miRNAs and TLR8 The Journal of Pain. 18: S13. DOI: 10.1016/J.Jpain.2017.02.053  0.687
2017 Campbell SL, Thompson PM, Ramachandran S, Case L, Dokholyan N, Tolbert C, Waterman CM. Role of PIP2-Dependent Membrane Interactions in Vinculin Activation, Motility and Force Transmission Biophysical Journal. 112: 479a. DOI: 10.1016/J.Bpj.2016.11.2594  0.595
2016 Thompson PM, Ramachandran S, Case LB, Tolbert CE, Tandon A, Pershad M, Dokholyan NV, Waterman CM, Campbell SL. A Structural Model for Vinculin Insertion into PIP2-Containing Membranes and the Effect of Insertion on Vinculin Activation and Localization. Structure (London, England : 1993). PMID 28089450 DOI: 10.1016/J.Str.2016.12.002  0.501
2016 Dagliyan O, Tarnawski M, Chu PH, Shirvanyants D, Schlichting I, Dokholyan NV, Hahn KM. Engineering extrinsic disorder to control protein activity in living cells. Science (New York, N.Y.). 354: 1441-1444. PMID 27980211 DOI: 10.1126/Science.Aah3404  0.779
2016 Fay JM, Zhu C, Proctor EA, Tao Y, Cui W, Ke H, Dokholyan NV. A Phosphomimetic Mutation Stabilizes SOD1 and Rescues Cell Viability in the Context of an ALS-Associated Mutation. Structure (London, England : 1993). PMID 27667694 DOI: 10.1016/J.Str.2016.08.011  0.64
2016 Convertino M, Das J, Dokholyan NV. Pharmacological chaperones: design and development of new therapeutic strategies for the treatment of conformational diseases. Acs Chemical Biology. PMID 27097127 DOI: 10.1021/Acschembio.6B00195  0.732
2016 Convertino M, Dokholyan NV. Computational Modeling of Small Molecule Ligand Binding Interactions and Affinities. Methods in Molecular Biology (Clifton, N.J.). 1414: 23-32. PMID 27094283 DOI: 10.1007/978-1-4939-3569-7_2  0.716
2016 Politi R, Convertino M, Popov K, Dokholyan NV, Tropsha A. Docking and Scoring With Target-Specific Pose Classifier Succeeds in Native-Like Pose Identification But Not Binding Affinity Prediction In The CSAR 2014 Benchmark Exercise. Journal of Chemical Information and Modeling. PMID 27050767 DOI: 10.1021/Acs.Jcim.5B00751  0.698
2016 Dokholyan NV. Controlling Allosteric Networks in Proteins. Chemical Reviews. PMID 26894745 DOI: 10.1021/acs.chemrev.5b00544  0.305
2016 Hadi-Alijanvand H, Proctor EA, Ding F, Dokholyan NV, Moosavi-Movahedi AA. A hidden aggregation-prone structure in the heart of hypoxia inducible factor prolyl hydroxylase. Proteins. PMID 26868435 DOI: 10.1002/Prot.25011  0.748
2016 Williams B, Convertino M, Das J, Dokholyan NV. P2-068: Rational Design of APOE4 Mutants as a Tool for Cellular Studies in Alzheimer’s Disease Alzheimer's & Dementia. 12: P634-P634. DOI: 10.1016/J.Jalz.2016.06.1273  0.678
2015 Proctor EA, Fee L, Tao Y, Redler RL, Fay JM, Zhang Y, Lv Z, Mercer IP, Deshmukh M, Lyubchenko YL, Dokholyan NV. Nonnative SOD1 trimer is toxic to motor neurons in a model of amyotrophic lateral sclerosis. Proceedings of the National Academy of Sciences of the United States of America. PMID 26719414 DOI: 10.1073/Pnas.1516725113  0.634
2015 Shobair M, Dagliyan O, Kota P, Dang YL, He H, Stutts MJ, Dokholyan NV. Gain-of-function mutation W493R in the epithelial sodium channel allosterically reconfigures intersubunit coupling. The Journal of Biological Chemistry. PMID 26668308 DOI: 10.1074/Jbc.M115.678052  0.797
2015 Samoshkin A, Convertino M, Viet CT, Wieskopf JS, Kambur O, Marcovitz J, Patel P, Stone LS, Kalso E, Mogil JS, Schmidt BL, Maixner W, Dokholyan NV, Diatchenko L. Structural and functional interactions between six-transmembrane μ-opioid receptors and β2-adrenoreceptors modulate opioid signaling. Scientific Reports. 5: 18198. PMID 26657998 DOI: 10.1038/Srep18198  0.74
2015 Proctor EA, Dokholyan NV. Applications of Discrete Molecular Dynamics in biology and medicine. Current Opinion in Structural Biology. 37: 9-13. PMID 26638022 DOI: 10.1016/J.Sbi.2015.11.001  0.697
2015 Convertino M, Samoshkin A, Viet CT, Gauthier J, Li Fraine SP, Sharif-Naeini R, Schmidt BL, Maixner W, Diatchenko L, Dokholyan NV. Differential Regulation of 6- and 7-Transmembrane Helix Variants of μ-Opioid Receptor in Response to Morphine Stimulation. Plos One. 10: e0142826. PMID 26554831 DOI: 10.1371/Journal.Pone.0142826  0.752
2015 Williams Ii B, Convertino M, Das J, Dokholyan NV. ApoE4-specific Misfolded Intermediate Identified by Molecular Dynamics Simulations. Plos Computational Biology. 11: e1004359. PMID 26506597 DOI: 10.1371/Journal.Pcbi.1004359  0.699
2015 Martin LJ, Piltonen MH, Gauthier J, Convertino M, Acland EL, Dokholyan NV, Mogil JS, Diatchenko L, Maixner W. Differences in the antinociceptive effects and binding properties of propranolol and bupranolol enantiomers. The Journal of Pain : Official Journal of the American Pain Society. PMID 26456674 DOI: 10.1016/J.Jpain.2015.09.004  0.731
2015 Meloto CB, Segall SK, Smith S, Parisien M, Shabalina SA, Rizzatti-Barbosa CM, Gauthier J, Tsao D, Convertino M, Piltonen MH, Slade GD, Fillingim RB, Greenspan JD, Ohrbach R, Knott C, ... ... Dokholyan NV, et al. COMT gene locus: new functional variants. Pain. 156: 2072-83. PMID 26207649 DOI: 10.1097/J.Pain.0000000000000273  0.768
2015 Wang L, Xie L, Ramachandran S, Lee Y, Yan Z, Zhou L, Krajewski K, Liu F, Zhu C, Chen DJ, Strahl BD, Jin J, Dokholyan NV, Chen X. Non-canonical Bromodomain within DNA-PKcs Promotes DNA Damage Response and Radioresistance through Recognizing an IR-Induced Acetyl-Lysine on H2AX. Chemistry & Biology. PMID 26119999 DOI: 10.1016/J.Chembiol.2015.05.014  0.448
2015 Miao Z, Adamiak RW, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cheng C, Chojnowski G, Chou FC, Cordero P, Cruz JA, Ferré-D'Amaré AR, Das R, Ding F, Dokholyan NV, et al. RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures. Rna (New York, N.Y.). 21: 1066-84. PMID 25883046 DOI: 10.1261/Rna.049502.114  0.463
2015 Proctor EA, Kota P, Aleksandrov AA, He L, Riordan JR, Dokholyan NV. Rational Coupled Dynamics Network Manipulation Rescues Disease-Relevant Mutant Cystic Fibrosis Transmembrane Conductance Regulator. Chemical Science (Royal Society of Chemistry : 2010). 6: 1237-1246. PMID 25685315 DOI: 10.1039/C4Sc01320D  0.803
2015 Convertino M, Samoshkin A, Gauthier J, Gold MS, Maixner W, Dokholyan NV, Diatchenko L. μ-Opioid receptor 6-transmembrane isoform: A potential therapeutic target for new effective opioids. Progress in Neuro-Psychopharmacology & Biological Psychiatry. 62: 61-7. PMID 25485963 DOI: 10.1016/J.Pnpbp.2014.11.009  0.74
2015 Thompson PM, Lee HT, Kim L, Ramachandran S, Tandon A, Mendez-Giraldez R, Alushin GM, Dokholyan NV, Campbell SL. New Models for Regulation of Vinculin by Actin and Phospholipids Biophysical Journal. 108: 508a-509a. DOI: 10.1016/J.Bpj.2014.11.2784  0.507
2015 Dickens O, Mendez-Giraldez R, Dokholyan N. Modeling the Calcium and Integrin Binding Protein 2 Biophysical Journal. 108: 213a. DOI: 10.1016/J.Bpj.2014.11.1178  0.34
2014 Homan PJ, Tandon A, Rice GM, Ding F, Dokholyan NV, Weeks KM. RNA tertiary structure analysis by 2'-hydroxyl molecular interference. Biochemistry. 53: 6825-33. PMID 25341083 DOI: 10.1021/Bi501218G  0.475
2014 Hasan SS, Proctor EA, Yamashita E, Dokholyan NV, Cramer WA. Traffic within the cytochrome b6f lipoprotein complex: gating of the quinone portal. Biophysical Journal. 107: 1620-8. PMID 25296314 DOI: 10.1016/J.Bpj.2014.08.003  0.642
2014 Nedd S, Redler RL, Proctor EA, Dokholyan NV, Alexandrova AN. Cu,Zn-superoxide dismutase without Zn is folded but catalytically inactive. Journal of Molecular Biology. 426: 4112-24. PMID 25083917 DOI: 10.1016/J.Jmb.2014.07.016  0.648
2014 Kota P, Buchner G, Chakraborty H, Dang YL, He H, Garcia GJ, Kubelka J, Gentzsch M, Stutts MJ, Dokholyan NV. The N-terminal domain allosterically regulates cleavage and activation of the epithelial sodium channel. The Journal of Biological Chemistry. 289: 23029-42. PMID 24973914 DOI: 10.1074/Jbc.M114.570952  0.657
2014 Shirvanyants D, Ramachandran S, Mei Y, Xu L, Meissner G, Dokholyan NV. Pore dynamics and conductance of RyR1 transmembrane domain. Biophysical Journal. 106: 2375-84. PMID 24896116 DOI: 10.1016/J.Bpj.2014.04.023  0.518
2014 Szöllősi D, Horváth T, Han KH, Dokholyan NV, Tompa P, Kalmár L, Hegedűs T. Discrete molecular dynamics can predict helical prestructured motifs in disordered proteins. Plos One. 9: e95795. PMID 24763499 DOI: 10.1371/journal.pone.0095795  0.304
2014 Thompson PM, Tolbert CE, Shen K, Kota P, Palmer SM, Plevock KM, Orlova A, Galkin VE, Burridge K, Egelman EH, Dokholyan NV, Superfine R, Campbell SL. Identification of an actin binding surface on vinculin that mediates mechanical cell and focal adhesion properties. Structure (London, England : 1993). 22: 697-706. PMID 24685146 DOI: 10.1016/J.Str.2014.03.002  0.647
2014 Furukawa Y, Teraguchi S, Ikegami T, Dagliyan O, Jin L, Hall D, Dokholyan NV, Namba K, Akira S, Kurosaki T, Baba Y, Standley DM. Intrinsic disorder mediates cooperative signal transduction in STIM1. Journal of Molecular Biology. 426: 2082-97. PMID 24650897 DOI: 10.1016/J.Jmb.2014.03.006  0.697
2014 Redler RL, Shirvanyants D, Dagliyan O, Ding F, Kim DN, Kota P, Proctor EA, Ramachandran S, Tandon A, Dokholyan NV. Computational approaches to understanding protein aggregation in neurodegeneration. Journal of Molecular Cell Biology. 6: 104-15. PMID 24620031 DOI: 10.1093/Jmcb/Mju007  0.799
2014 He L, Kota P, Aleksandrov AA, Cui L, Jensen T, Dokholyan NV, Riordan JR. Correctors of δF508 CFTR restore global conformational maturation without thermally stabilizing the mutant protein (FASEB Journal (2013) 27 (536 -545) DOI:10.1096/fj.12-216119) Faseb Journal. 28: 2737. DOI: 10.1096/Fj.12-216119Err  0.661
2014 Nedd S, Redler RL, Proctor EA, Dokholyan NV, Alexandrova AN. Cu,Zn-superoxide dismutase without Zn is folded but catalytically inactive Journal of Molecular Biology. 426: 4112-4124. DOI: 10.1016/j.jmb.2014.07.016  0.59
2014 Dokholyan NV, Redler RL, Proctor EA, Ding FV, Wilcox K, Caplow M. Post-Translational Modifications Promote Formation of SOD1 Oligomers with Potential Toxicity in ALS Biophysical Journal. 106: 33a-34a. DOI: 10.1016/J.Bpj.2013.11.258  0.793
2014 Wang C, Kota P, Yang Z, Aleksandrov A, An J, Forouhar F, Boel G, Dokholyan N, Riordan J, Brouillette C, Hunt J. A Robust High-Throughput Assay for Thermodynamic Correctors of the Predominant Molecular Defect Causing Cystic Fibrosis Biophysical Journal. 106: 432a. DOI: 10.1016/J.Bpj.2013.11.2433  0.701
2013 Freeman TC, Black JL, Bray HG, Dagliyan O, Wu YI, Tripathy A, Dokholyan NV, Leisner TM, Parise LV. Identification of novel integrin binding partners for calcium and integrin binding protein 1 (CIB1): structural and thermodynamic basis of CIB1 promiscuity. Biochemistry. 52: 7082-90. PMID 24011356 DOI: 10.1021/Bi400678Y  0.699
2013 Barison N, Cendron L, Loconte V, Proctor EA, Dokholyan NV, Zanotti G. Protein HP1028 from the human pathogen Helicobacter pylori belongs to the lipocalin family. Acta Crystallographica. Section D, Biological Crystallography. 69: 1387-94. PMID 23897462 DOI: 10.1107/S0907444913008160  0.682
2013 Fourches D, Muratov E, Ding F, Dokholyan NV, Tropsha A. Predicting binding affinity of CSAR ligands using both structure-based and ligand-based approaches. Journal of Chemical Information and Modeling. 53: 1915-22. PMID 23809015 DOI: 10.1021/Ci400216Q  0.471
2013 Kummer L, Hsu CW, Dagliyan O, MacNevin C, Kaufholz M, Zimmermann B, Dokholyan NV, Hahn KM, Plückthun A. Knowledge-based design of a biosensor to quantify localized ERK activation in living cells. Chemistry & Biology. 20: 847-56. PMID 23790495 DOI: 10.1016/J.Chembiol.2013.04.016  0.751
2013 Hudson NE, Ding F, Bucay I, O'Brien ET, Gorkun OV, Superfine R, Lord ST, Dokholyan NV, Falvo MR. Submillisecond elastic recoil reveals molecular origins of fibrin fiber mechanics. Biophysical Journal. 104: 2671-80. PMID 23790375 DOI: 10.1016/J.Bpj.2013.04.052  0.479
2013 Dagliyan O, Shirvanyants D, Karginov AV, Ding F, Fee L, Chandrasekaran SN, Freisinger CM, Smolen GA, Huttenlocher A, Hahn KM, Dokholyan NV. Rational design of a ligand-controlled protein conformational switch. Proceedings of the National Academy of Sciences of the United States of America. 110: 6800-4. PMID 23569285 DOI: 10.1073/Pnas.1218319110  0.801
2013 Chong PA, Kota P, Dokholyan NV, Forman-Kay JD. Dynamics intrinsic to cystic fibrosis transmembrane conductance regulator function and stability. Cold Spring Harbor Perspectives in Medicine. 3: a009522. PMID 23457292 DOI: 10.1101/Cshperspect.A009522  0.675
2013 Ramachandran S, Chakraborty A, Xu L, Mei Y, Samsó M, Dokholyan NV, Meissner G. Structural determinants of skeletal muscle ryanodine receptor gating. The Journal of Biological Chemistry. 288: 6154-65. PMID 23319589 DOI: 10.1074/Jbc.M112.433789  0.51
2013 Ramachandran S, Ding F, Weeks KM, Dokholyan NV. Statistical analysis of SHAPE-directed RNA secondary structure modeling. Biochemistry. 52: 596-9. PMID 23286327 DOI: 10.1021/Bi300756S  0.616
2013 Proctor EA, Kota P, Demarest SJ, Caravella JA, Dokholyan NV. Highly covarying residues have a functional role in antibody constant domains. Proteins. 81: 884-95. PMID 23280585 DOI: 10.1002/Prot.24247  0.786
2013 Ding F, Dokholyan NV. Incorporating backbone flexibility in MedusaDock improves ligand-binding pose prediction in the CSAR2011 docking benchmark. Journal of Chemical Information and Modeling. 53: 1871-9. PMID 23237273 DOI: 10.1021/Ci300478Y  0.475
2013 Proctor EA, Kota P, Demarest SJ, Caravella JA, Dokholyan NV. Metric to distinguish closely related domain families using sequence information. Journal of Molecular Biology. 425: 475-8. PMID 23219465 DOI: 10.1016/J.Jmb.2012.11.031  0.769
2013 He L, Kota P, Aleksandrov AA, Cui L, Jensen T, Dokholyan NV, Riordan JR. Correctors of ΔF508 CFTR restore global conformational maturation without thermally stabilizing the mutant protein. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 27: 536-45. PMID 23104983 DOI: 10.1096/Fj.12-216119  0.665
2013 Hadi-Alijanvand H, Proctor EA, Goliaei B, Dokholyan NV, Moosavi-Movahedi AA. Correction: Thermal unfolding pathway of PHD2 catalytic domain in three different PHD2 species: Computational approaches (PLoS ONE) Plos One. 8. DOI: 10.1371/Annotation/C414C3Ec-B64E-4Cf4-Bff2-7Bb7B3Abb558  0.65
2013 Chu P, Karginov AV, Shirvanyants DG, Dokholyan NV, Hahn KM. Generation of a Light Inhibited Src Kinase through Insertion of LOV into the Catalytic Domain Biophysical Journal. 104: 679a. DOI: 10.1016/J.Bpj.2012.11.3750  0.498
2013 Diaz JR, Dokholyan N, Redler R. Is Protein Destabilization a Widespread Factor in Genetic Disease? Biophysical Journal. 104: 565a. DOI: 10.1016/J.Bpj.2012.11.3133  0.357
2012 Cole DI, Legassie JD, Bonifacio LN, Sekaran VG, Ding F, Dokholyan NV, Jarstfer MB. New models of Tetrahymena telomerase RNA from experimentally derived constraints and modeling. Journal of the American Chemical Society. 134: 20070-80. PMID 23163801 DOI: 10.1021/Ja305636U  0.519
2012 Hadi-Alijanvand H, Proctor EA, Goliaei B, Dokholyan NV, Moosavi-Movahedi AA. Thermal unfolding pathway of PHD2 catalytic domain in three different PHD2 species: computational approaches. Plos One. 7: e47061. PMID 23077544 DOI: 10.1371/Journal.Pone.0047061  0.685
2012 Ramachandran S, Temple B, Alexandrova AN, Chaney SG, Dokholyan NV. Recognition of platinum-DNA adducts by HMGB1a. Biochemistry. 51: 7608-17. PMID 22950413 DOI: 10.1021/Bi3008577  0.465
2012 Sparta M, Shirvanyants D, Ding F, Dokholyan NV, Alexandrova AN. Hybrid dynamics simulation engine for metalloproteins Biophysical Journal. 103: 767-776. PMID 22947938 DOI: 10.1016/J.Bpj.2012.06.024  0.532
2012 Nakayama T, Butler JS, Sehgal A, Severgnini M, Racie T, Sharman J, Ding F, Morskaya SS, Brodsky J, Tchangov L, Kosovrasti V, Meys M, Nechev L, Wang G, Peng CG, ... ... Dokholyan NV, et al. Harnessing a physiologic mechanism for siRNA delivery with mimetic lipoprotein particles. Molecular Therapy : the Journal of the American Society of Gene Therapy. 20: 1582-9. PMID 22850721 DOI: 10.1038/Mt.2012.33  0.425
2012 Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, et al. The interface of protein structure, protein biophysics, and molecular evolution. Protein Science : a Publication of the Protein Society. 21: 769-85. PMID 22528593 DOI: 10.1002/Pro.2071  0.547
2012 Ding F, Lavender CA, Weeks KM, Dokholyan NV. Three-dimensional RNA structure refinement by hydroxyl radical probing. Nature Methods. 9: 603-8. PMID 22504587 DOI: 10.1038/Nmeth.1976  0.469
2012 Tsao D, Wieskopf JS, Rashid N, Sorge RE, Redler RL, Segall SK, Mogil JS, Maixner W, Dokholyan NV, Diatchenko L. Serotonin-induced hypersensitivity via inhibition of catechol O-methyltransferase activity. Molecular Pain. 8: 25. PMID 22500608 DOI: 10.1186/1744-8069-8-25  0.65
2012 Kota P, García-Caballero A, Dang H, Gentzsch M, Stutts MJ, Dokholyan NV. Energetic and structural basis for activation of the epithelial sodium channel by matriptase. Biochemistry. 51: 3460-9. PMID 22471557 DOI: 10.1021/Bi2014773  0.655
2012 Aleksandrov AA, Kota P, Cui L, Jensen T, Alekseev AE, Reyes S, He L, Gentzsch M, Aleksandrov LA, Dokholyan NV, Riordan JR. Allosteric modulation balances thermodynamic stability and restores function of ΔF508 CFTR. Journal of Molecular Biology. 419: 41-60. PMID 22406676 DOI: 10.1016/J.Jmb.2012.03.001  0.676
2012 Pulicherla N, Kota P, Dokholyan NV, Asokan A. Intra- and inter-subunit disulfide bond formation is nonessential in adeno-associated viral capsids. Plos One. 7: e32163. PMID 22389684 DOI: 10.1371/Journal.Pone.0032163  0.678
2012 Cruz JA, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cao S, Das R, Ding F, Dokholyan NV, Flores SC, Huang L, Lavender CA, Lisi V, Major F, Mikolajczak K, et al. RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. Rna (New York, N.Y.). 18: 610-25. PMID 22361291 DOI: 10.1261/Rna.031054.111  0.446
2012 Shirvanyants D, Ding F, Tsao D, Ramachandran S, Dokholyan NV. Discrete molecular dynamics: an efficient and versatile simulation method for fine protein characterization. The Journal of Physical Chemistry. B. 116: 8375-82. PMID 22280505 DOI: 10.1021/Jp2114576  0.768
2012 Proctor EA, Yin S, Tropsha A, Dokholyan NV. Discrete molecular dynamics distinguishes nativelike binding poses from decoys in difficult targets. Biophysical Journal. 102: 144-51. PMID 22225808 DOI: 10.1016/J.Bpj.2011.11.4008  0.681
2012 Ding F, Furukawa Y, Nukina N, Dokholyan NV. Local unfolding of Cu, Zn superoxide dismutase monomer determines the morphology of fibrillar aggregates. Journal of Molecular Biology. 421: 548-60. PMID 22210350 DOI: 10.1016/J.Jmb.2011.12.029  0.519
2012 Shobair M, Cole D, Ding F, Jarstfer M, Dokholyan N. Computational Modeling of Telomerase in Action Biophysical Journal. 102: 732a. DOI: 10.1016/J.Bpj.2011.11.3972  0.559
2012 Gyimesi G, Ramachandran S, Kota P, Dokholyan NV, Sarkadi B, Hegedűs T. Corrigendum to “ATP hydrolysis at one of the two sites in ABC transporters initiates transport related conformational transitions” [Biochim. Biophys. Acta 1808 (2011) 2954–2964] Biochimica Et Biophysica Acta (Bba) - Biomembranes. 1818: 1435. DOI: 10.1016/J.Bbamem.2012.01.004  0.687
2012 Proctor EA, Ding F, Dokholyan NV. ChemInform Abstract: Discrete Molecular Dynamics Cheminform. 43: no-no. DOI: 10.1002/chin.201240278  0.611
2011 Dagliyan O, Proctor EA, D'Auria KM, Ding F, Dokholyan NV. Structural and dynamic determinants of protein-peptide recognition. Structure (London, England : 1993). 19: 1837-45. PMID 22153506 DOI: 10.1016/J.Str.2011.09.014  0.793
2011 Serohijos AW, Yin S, Ding F, Gauthier J, Gibson DG, Maixner W, Dokholyan NV, Diatchenko L. Structural basis for μ-opioid receptor binding and activation. Structure (London, England : 1993). 19: 1683-90. PMID 22078567 DOI: 10.1016/J.Str.2011.08.003  0.795
2011 Tsao D, Diatchenko L, Dokholyan NV. Structural mechanism of S-adenosyl methionine binding to catechol O-methyltransferase. Plos One. 6: e24287. PMID 21904625 DOI: 10.1371/Journal.Pone.0024287  0.692
2011 Bhattacharyya D, Ramachandran S, Sharma S, Pathmasiri W, King CL, Baskerville-Abraham I, Boysen G, Swenberg JA, Campbell SL, Dokholyan NV, Chaney SG. Flanking bases influence the nature of DNA distortion by platinum 1,2-intrastrand (GG) cross-links. Plos One. 6: e23582. PMID 21853154 DOI: 10.1371/Journal.Pone.0023582  0.605
2011 Gyimesi G, Ramachandran S, Kota P, Dokholyan NV, Sarkadi B, Hegedus T. ATP hydrolysis at one of the two sites in ABC transporters initiates transport related conformational transitions. Biochimica Et Biophysica Acta. 1808: 2954-64. PMID 21840296 DOI: 10.1016/J.Bbamem.2011.07.038  0.736
2011 Redler RL, Wilcox KC, Proctor EA, Fee L, Caplow M, Dokholyan NV. Glutathionylation at Cys-111 induces dissociation of wild type and FALS mutant SOD1 dimers. Biochemistry. 50: 7057-66. PMID 21739997 DOI: 10.1021/Bi200614Y  0.789
2011 Tsao D, Liu S, Dokholyan NV. Regioselectivity of Catechol O-Methyltransferase Confers Enhancement of Catalytic Activity. Chemical Physics Letters. 506: 135-138. PMID 21731105 DOI: 10.1016/J.Cplett.2011.03.048  0.526
2011 Tsygankov D, Serohijos AW, Dokholyan NV, Elston TC. A physical model reveals the mechanochemistry responsible for dynein's processive motion. Biophysical Journal. 101: 144-50. PMID 21723824 DOI: 10.1016/J.Bpj.2011.05.043  0.71
2011 Kota P, Ding F, Ramachandran S, Dokholyan NV. Gaia: automated quality assessment of protein structure models. Bioinformatics (Oxford, England). 27: 2209-15. PMID 21700672 DOI: 10.1093/Bioinformatics/Btr374  0.782
2011 Serohijos AW, Thibodeau PH, Dokholyan NV. Molecular modeling tools and approaches for CFTR and cystic fibrosis. Methods in Molecular Biology (Clifton, N.J.). 741: 347-63. PMID 21594796 DOI: 10.1007/978-1-61779-117-8_23  0.694
2011 Tsao D, Shabalina SA, Gauthier J, Dokholyan NV, Diatchenko L. Disruptive mRNA folding increases translational efficiency of catechol-O-methyltransferase variant. Nucleic Acids Research. 39: 6201-12. PMID 21486747 DOI: 10.1016/J.Jpain.2011.02.129  0.714
2011 Proctor EA, Ding F, Dokholyan NV. Structural and thermodynamic effects of post-translational modifications in mutant and wild type Cu, Zn superoxide dismutase. Journal of Molecular Biology. 408: 555-67. PMID 21396374 DOI: 10.1016/J.Jmb.2011.03.004  0.73
2011 Hadi-Alijanvand H, Rouhani M, Proctor EA, Dokholyan NV, Moosavi-Movahedi AA. A folding pathway-dependent score to recognize membrane proteins. Plos One. 6: e16778. PMID 21390303 DOI: 10.1371/Journal.Pone.0016778  0.663
2011 Ramachandran S, Vogel L, Strahl BD, Dokholyan NV. Thermodynamic stability of histone H3 is a necessary but not sufficient driving force for its evolutionary conservation. Plos Computational Biology. 7: e1001042. PMID 21253558 DOI: 10.1371/Journal.Pcbi.1001042  0.478
2011 Kota P, Dokholyan NV. Approaches for probing the sequence space of substrates recognized by molecular chaperones. Methods (San Diego, Calif.). 53: 318-24. PMID 21195183 DOI: 10.1016/J.Ymeth.2010.12.034  0.671
2011 Karginov AV, Zou Y, Shirvanyants D, Kota P, Dokholyan NV, Young DD, Hahn KM, Deiters A. Light regulation of protein dimerization and kinase activity in living cells using photocaged rapamycin and engineered FKBP. Journal of the American Chemical Society. 133: 420-3. PMID 21162531 DOI: 10.1021/Ja109630V  0.725
2011 Ramachandran S, Kota P, Ding F, Dokholyan NV. Automated minimization of steric clashes in protein structures. Proteins. 79: 261-70. PMID 21058396 DOI: 10.1002/Prot.22879  0.793
2010 Ding F, Yin S, Dokholyan NV. Rapid flexible docking using a stochastic rotamer library of ligands. Journal of Chemical Information and Modeling. 50: 1623-32. PMID 20712341 DOI: 10.1021/Ci100218T  0.46
2010 Tsao D, Minton AP, Dokholyan NV. A didactic model of macromolecular crowding effects on protein folding. Plos One. 5: e11936. PMID 20689808 DOI: 10.1371/Journal.Pone.0011936  0.606
2010 Yin S, Ding F, Dokholyan NV. Computational evaluation of protein stability change upon mutations. Methods in Molecular Biology (Clifton, N.J.). 634: 189-201. PMID 20676985 DOI: 10.1007/978-1-60761-652-8_14  0.533
2010 Karginov AV, Ding F, Kota P, Dokholyan NV, Hahn KM. Engineered allosteric activation of kinases in living cells. Nature Biotechnology. 28: 743-7. PMID 20581846 DOI: 10.1038/Nbt.1639  0.779
2010 Aleksandrov AA, Kota P, Aleksandrov LA, He L, Jensen T, Cui L, Gentzsch M, Dokholyan NV, Riordan JR. Regulatory insertion removal restores maturation, stability and function of DeltaF508 CFTR. Journal of Molecular Biology. 401: 194-210. PMID 20561529 DOI: 10.1016/J.Jmb.2010.06.019  0.664
2010 Lavender CA, Ding F, Dokholyan NV, Weeks KM. Robust and generic RNA modeling using inferred constraints: a structure for the hepatitis C virus IRES pseudoknot domain. Biochemistry. 49: 4931-3. PMID 20545364 DOI: 10.1021/Bi100142Y  0.494
2010 Hajdin CE, Ding F, Dokholyan NV, Weeks KM. On the significance of an RNA tertiary structure prediction. Rna (New York, N.Y.). 16: 1340-9. PMID 20498460 DOI: 10.1261/Rna.1837410  0.475
2010 Lakhani VV, Ding F, Dokholyan NV. Polyglutamine induced misfolding of huntingtin exon1 is modulated by the flanking sequences. Plos Computational Biology. 6: e1000772. PMID 20442863 DOI: 10.1371/Journal.Pcbi.1000772  0.515
2010 Gaillard EA, Kota P, Gentzsch M, Dokholyan NV, Stutts MJ, Tarran R. Regulation of the epithelial Na+ channel and airway surface liquid volume by serine proteases. PflüGers Archiv : European Journal of Physiology. 460: 1-17. PMID 20401730 DOI: 10.1007/S00424-010-0827-Z  0.616
2010 Tsao D, Dokholyan NV. Macromolecular crowding induces polypeptide compaction and decreases folding cooperativity. Physical Chemistry Chemical Physics : Pccp. 12: 3491-500. PMID 20355290 DOI: 10.1039/B924236H  0.635
2010 Kesner BA, Milgram SL, Temple BR, Dokholyan NV. Isoform divergence of the filamin family of proteins. Molecular Biology and Evolution. 27: 283-95. PMID 19805437 DOI: 10.1093/Molbev/Msp236  0.779
2010 Kesner BA, Ding F, Temple BR, Dokholyan NV. N-terminal strands of filamin Ig domains act as a conformational switch under biological forces. Proteins. 78: 12-24. PMID 19514078 DOI: 10.1002/Prot.22479  0.797
2010 Lavender CA, Ding F, Dokholyan NV, Weeks KM. Correction to Robust and Generic RNA Modeling Using Inferred Constraints: A Structure for the Hepatitis C Virus IRES Pseudoknot Domain Biochemistry. 49: 5968-5968. DOI: 10.1021/Bi100935C  0.45
2010 Tsygankov D, Serohijos AW, Dokholyan NV, Elston T. A Coupling of Structural and Kinetic Models Reveals the Stepping Mechanics of Dynein Biophysical Journal. 98: 613a. DOI: 10.1016/J.Bpj.2009.12.3345  0.712
2009 Yin S, Proctor EA, Lugovskoy AA, Dokholyan NV. Fast screening of protein surfaces using geometric invariant fingerprints. Proceedings of the National Academy of Sciences of the United States of America. 106: 16622-6. PMID 19805347 DOI: 10.1073/Pnas.0906146106  0.691
2009 Kota P, Summers DW, Ren HY, Cyr DM, Dokholyan NV. Identification of a consensus motif in substrates bound by a Type I Hsp40. Proceedings of the National Academy of Sciences of the United States of America. 106: 11073-8. PMID 19549854 DOI: 10.1073/Pnas.0900746106  0.686
2009 Serohijos AW, Tsygankov D, Liu S, Elston TC, Dokholyan NV. Multiscale approaches for studying energy transduction in dynein. Physical Chemistry Chemical Physics : Pccp. 11: 4840-50. PMID 19506759 DOI: 10.1039/B902028D  0.692
2009 Ramachandran S, Serohijos AW, Xu L, Meissner G, Dokholyan NV. A structural model of the pore-forming region of the skeletal muscle ryanodine receptor (RyR1). Plos Computational Biology. 5: e1000367. PMID 19390614 DOI: 10.1371/Journal.Pcbi.1000367  0.745
2009 Wilcox KC, Zhou L, Jordon JK, Huang Y, Yu Y, Redler RL, Chen X, Caplow M, Dokholyan NV. Modifications of superoxide dismutase (SOD1) in human erythrocytes: a possible role in amyotrophic lateral sclerosis. The Journal of Biological Chemistry. 284: 13940-7. PMID 19299510 DOI: 10.1074/Jbc.M809687200  0.703
2009 Ramachandran S, Temple BR, Chaney SG, Dokholyan NV. Structural basis for the sequence-dependent effects of platinum-DNA adducts. Nucleic Acids Research. 37: 2434-48. PMID 19255091 DOI: 10.1093/Nar/Gkp029  0.511
2009 Gherghe CM, Leonard CW, Ding F, Dokholyan NV, Weeks KM. Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics. Journal of the American Chemical Society. 131: 2541-6. PMID 19193004 DOI: 10.1021/Ja805460E  0.489
2009 Torres MP, Lee MJ, Ding F, Purbeck C, Kuhlman B, Dokholyan NV, Dohlman HG. G Protein Mono-ubiquitination by the Rsp5 Ubiquitin Ligase. The Journal of Biological Chemistry. 284: 8940-50. PMID 19176477 DOI: 10.1074/Jbc.M809058200  0.515
2009 Tsygankov D, Serohijos AW, Dokholyan NV, Elston TC. Kinetic models for the coordinated stepping of cytoplasmic dynein. The Journal of Chemical Physics. 130: 025101. PMID 19154055 DOI: 10.1063/1.3050098  0.699
2009 Petrotchenko EV, Xiao K, Cable J, Chen Y, Dokholyan NV, Borchers CH. BiPS, a photocleavable, isotopically coded, fluorescent cross-linker for structural proteomics. Molecular & Cellular Proteomics : McP. 8: 273-86. PMID 18838738 DOI: 10.1074/Mcp.M800265-Mcp200  0.358
2009 Meissner G, Pasek DA, Yamaguchi N, Ramachandran S, Dokholyan NV, Tripathy A. Thermodynamics of calmodulin binding to cardiac and skeletal muscle ryanodine receptor ion channels. Proteins. 74: 207-11. PMID 18618700 DOI: 10.1002/Prot.22148  0.456
2009 Ramachandran S, Serohijos AW, Xu L, Meissner G, Dokholyan NV. Ryanodine Receptor Pore Structure and Function Biophysical Journal. 96: 107a. DOI: 10.1016/J.Bpj.2008.12.462  0.75
2009 Riordan JR, Dokholyan N, Serohijos A, Cui L, Hegedus T, Aleksandrov L, He L, Aleksandrov AA. Influence of DF508 on CFTR assembly and function Pediatric Pulmonology. 44: 122-123. DOI: 10.1002/ppul.20948  0.659
2008 Ding F, Dokholyan NV. Dynamical roles of metal ions and the disulfide bond in Cu, Zn superoxide dismutase folding and aggregation. Proceedings of the National Academy of Sciences of the United States of America. 105: 19696-701. PMID 19052230 DOI: 10.1073/Pnas.0803266105  0.486
2008 Hao J, Serohijos AW, Newton G, Tassone G, Wang Z, Sgroi DC, Dokholyan NV, Basilion JP. Identification and rational redesign of peptide ligands to CRIP1, a novel biomarker for cancers. Plos Computational Biology. 4: e1000138. PMID 18670594 DOI: 10.1371/Journal.Pcbi.1000138  0.684
2008 He L, Aleksandrov AA, Serohijos AW, Hegedus T, Aleksandrov LA, Cui L, Dokholyan NV, Riordan JR. Multiple membrane-cytoplasmic domain contacts in the cystic fibrosis transmembrane conductance regulator (CFTR) mediate regulation of channel gating. The Journal of Biological Chemistry. 283: 26383-90. PMID 18658148 DOI: 10.1074/jbc.M803894200  0.715
2008 Teotico DG, Frazier ML, Ding F, Dokholyan NV, Temple BR, Redinbo MR. Active nuclear receptors exhibit highly correlated AF-2 domain motions. Plos Computational Biology. 4: e1000111. PMID 18617990 DOI: 10.1371/Journal.Pcbi.1000111  0.473
2008 Ding F, Tsao D, Nie H, Dokholyan NV. Ab initio folding of proteins with all-atom discrete molecular dynamics. Structure (London, England : 1993). 16: 1010-8. PMID 18611374 DOI: 10.1016/J.Str.2008.03.013  0.719
2008 Sharma S, Ding F, Dokholyan NV. iFoldRNA: three-dimensional RNA structure prediction and folding. Bioinformatics (Oxford, England). 24: 1951-2. PMID 18579566 DOI: 10.1093/Bioinformatics/Btn328  0.596
2008 Sharma S, Ding F, Dokholyan NV. Probing protein aggregation using discrete molecular dynamics. Frontiers in Bioscience : a Journal and Virtual Library. 13: 4795-808. PMID 18508545 DOI: 10.2741/3039  0.657
2008 Chen Y, Dokholyan NV. Natural selection against protein aggregation on self-interacting and essential proteins in yeast, fly, and worm. Molecular Biology and Evolution. 25: 1530-3. PMID 18503047 DOI: 10.1093/Molbev/Msn122  0.438
2008 Serohijos AW, Hegedus T, Riordan JR, Dokholyan NV. Diminished self-chaperoning activity of the DeltaF508 mutant of CFTR results in protein misfolding. Plos Computational Biology. 4: e1000008. PMID 18463704 DOI: 10.1371/journal.pcbi.1000008  0.735
2008 Ding F, Sharma S, Chalasani P, Demidov VV, Broude NE, Dokholyan NV. Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. Rna (New York, N.Y.). 14: 1164-73. PMID 18456842 DOI: 10.1261/Rna.894608  0.609
2008 Hegedus T, Serohijos AW, Dokholyan NV, He L, Riordan JR. Computational studies reveal phosphorylation-dependent changes in the unstructured R domain of CFTR. Journal of Molecular Biology. 378: 1052-63. PMID 18423665 DOI: 10.1016/j.jmb.2008.03.033  0.712
2008 Serohijos AW, Hegedus T, Aleksandrov AA, He L, Cui L, Dokholyan NV, Riordan JR. Phenylalanine-508 mediates a cytoplasmic-membrane domain contact in the CFTR 3D structure crucial to assembly and channel function. Proceedings of the National Academy of Sciences of the United States of America. 105: 3256-61. PMID 18305154 DOI: 10.1073/pnas.0800254105  0.726
2008 Sharma S, Dokholyan NV. DNA sequence mediates nucleosome structure and stability. Biophysical Journal. 94: 1-3. PMID 17933872 DOI: 10.1529/Biophysj.107.119172  0.439
2008 Chen Y, Ding F, Nie H, Serohijos AW, Sharma S, Wilcox KC, Yin S, Dokholyan NV. Protein folding: then and now. Archives of Biochemistry and Biophysics. 469: 4-19. PMID 17585870 DOI: 10.1016/J.Abb.2007.05.014  0.805
2007 Khare SD, Dokholyan NV. Molecular mechanisms of polypeptide aggregation in human diseases. Current Protein & Peptide Science. 8: 573-9. PMID 18220844 DOI: 10.2174/138920307783018703  0.542
2007 Yin S, Ding F, Dokholyan NV. Modeling backbone flexibility improves protein stability estimation. Structure (London, England : 1993). 15: 1567-76. PMID 18073107 DOI: 10.1016/J.Str.2007.09.024  0.555
2007 Sharma S, Gong P, Temple B, Bhattacharyya D, Dokholyan NV, Chaney SG. Molecular dynamic simulations of cisplatin- and oxaliplatin-d(GG) intrastand cross-links reveal differences in their conformational dynamics. Journal of Molecular Biology. 373: 1123-40. PMID 17900616 DOI: 10.1016/J.Jmb.2007.07.079  0.462
2007 Lam AR, Borreguero JM, Ding F, Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich E. Parallel folding pathways in the SH3 domain protein. Journal of Molecular Biology. 373: 1348-60. PMID 17900612 DOI: 10.1016/J.Jmb.2007.08.032  0.82
2007 Barton S, Jacak R, Khare SD, Ding F, Dokholyan NV. The length dependence of the polyQ-mediated protein aggregation. The Journal of Biological Chemistry. 282: 25487-92. PMID 17591778 DOI: 10.1074/Jbc.M701600200  0.672
2007 Chen Y, Campbell SL, Dokholyan NV. Deciphering protein dynamics from NMR data using explicit structure sampling and selection. Biophysical Journal. 93: 2300-6. PMID 17557784 DOI: 10.1529/Biophysj.107.104174  0.444
2007 Chen Y, Ding F, Dokholyan NV. Fidelity of the protein structure reconstruction from inter-residue proximity constraints. The Journal of Physical Chemistry. B. 111: 7432-8. PMID 17542631 DOI: 10.1021/Jp068963T  0.609
2007 Yin S, Ding F, Dokholyan NV. Eris: an automated estimator of protein stability. Nature Methods. 4: 466-7. PMID 17538626 DOI: 10.1038/Nmeth0607-466  0.478
2007 Sharma S, Ding F, Dokholyan NV. Multiscale modeling of nucleosome dynamics. Biophysical Journal. 92: 1457-70. PMID 17142268 DOI: 10.1529/Biophysj.106.094805  0.601
2007 Sharma S, Ding F, Dokholyan NV. Multiscalar nucleosome dynamics in silico ‐ Role of DNA and histone tails The Faseb Journal. 21. DOI: 10.1096/Fasebj.21.5.A282-C  0.559
2007 Chen Y, Dokholyan NV. A molecular switch ‐ insights into allosteric control of vinculin function from in‐silico study of its large‐scale conformational dynamics The Faseb Journal. 21. DOI: 10.1096/Fasebj.21.5.A270  0.364
2007 Podobnik B, Shao J, Dokholyan NV, Zlatic V, Eugene Stanley H, Grosse I. Similarity and dissimilarity in correlations of genomic DNA Physica a: Statistical Mechanics and Its Applications. 373: 497-502. DOI: 10.1016/J.Physa.2006.05.041  0.542
2006 Serohijos AW, Chen Y, Ding F, Elston TC, Dokholyan NV. A structural model reveals energy transduction in dynein. Proceedings of the National Academy of Sciences of the United States of America. 103: 18540-5. PMID 17121997 DOI: 10.1073/Pnas.0602867103  0.772
2006 Khare SD, Caplow M, Dokholyan NV. FALS mutations in Cu, Zn superoxide dismutase destabilize the dimer and increase dimer dissociation propensity: a large-scale thermodynamic analysis. Amyloid : the International Journal of Experimental and Clinical Investigation : the Official Journal of the International Society of Amyloidosis. 13: 226-35. PMID 17107883 DOI: 10.1080/13506120600960486  0.489
2006 Sharma S, Ding F, Nie H, Watson D, Unnithan A, Lopp J, Pozefsky D, Dokholyan NV. iFold: a platform for interactive folding simulations of proteins. Bioinformatics (Oxford, England). 22: 2693-4. PMID 16940324 DOI: 10.1093/Bioinformatics/Btl460  0.666
2006 Chen Y, Dokholyan NV. Insights into allosteric control of vinculin function from its large scale conformational dynamics. The Journal of Biological Chemistry. 281: 29148-54. PMID 16891659 DOI: 10.1074/Jbc.M605512200  0.445
2006 Ding F, Dokholyan NV. Emergence of protein fold families through rational design. Plos Computational Biology. 2: e85. PMID 16839198 DOI: 10.1371/Journal.Pcbi.0020085  0.532
2006 Chen Y, Dokholyan NV. The coordinated evolution of yeast proteins is constrained by functional modularity. Trends in Genetics : Tig. 22: 416-9. PMID 16797778 DOI: 10.1016/J.Tig.2006.06.008  0.405
2006 Bloom K, Sharma S, Dokholyan NV. The path of DNA in the kinetochore. Current Biology : Cb. 16: R276-8. PMID 16631569 DOI: 10.1016/J.Cub.2006.03.054  0.364
2006 Khare SD, Dokholyan NV. Common dynamical signatures of familial amyotrophic lateral sclerosis-associated structurally diverse Cu, Zn superoxide dismutase mutants. Proceedings of the National Academy of Sciences of the United States of America. 103: 3147-52. PMID 16488975 DOI: 10.1073/pnas.0511266103  0.522
2006 Demidov VV, Dokholyan NV, Witte-Hoffmann C, Chalasani P, Yiu HW, Ding F, Yu Y, Cantor CR, Broude NE. Fast complementation of split fluorescent protein triggered by DNA hybridization. Proceedings of the National Academy of Sciences of the United States of America. 103: 2052-6. PMID 16461889 DOI: 10.1073/Pnas.0511078103  0.485
2006 Ding F, Prutzman KC, Campbell SL, Dokholyan NV. Topological determinants of protein domain swapping. Structure (London, England : 1993). 14: 5-14. PMID 16407060 DOI: 10.1016/J.Str.2005.09.008  0.56
2006 Ding F, Dokholyan NV. Correction: Emergence of Protein Fold Families through Rational Design Plos Computational Biology. 2: e149. DOI: 10.1371/Journal.Pcbi.0020149  0.498
2005 Chen Y, Dokholyan NV. A single disulfide bond differentiates aggregation pathways of beta2-microglobulin. Journal of Molecular Biology. 354: 473-82. PMID 16242719 DOI: 10.1016/J.Jmb.2005.09.075  0.374
2005 Ding F, LaRocque JJ, Dokholyan NV. Direct observation of protein folding, aggregation, and a prion-like conformational conversion. The Journal of Biological Chemistry. 280: 40235-40. PMID 16204250 DOI: 10.1074/Jbc.M506372200  0.507
2005 Khare SD, Ding F, Gwanmesia KN, Dokholyan NV. Molecular origin of polyglutamine aggregation in neurodegenerative diseases. Plos Computational Biology. 1: 230-5. PMID 16158094 DOI: 10.1371/Journal.Pcbi.0010030  0.636
2005 Khare SD, Wilcox KC, Gong P, Dokholyan NV. Sequence and structural determinants of Cu, Zn superoxide dismutase aggregation. Proteins. 61: 617-32. PMID 16152647 DOI: 10.1002/Prot.20629  0.773
2005 Ding F, Dokholyan NV. Simple but predictive protein models. Trends in Biotechnology. 23: 450-5. PMID 16038997 DOI: 10.1016/J.Tibtech.2005.07.001  0.517
2005 Ding F, Jha RK, Dokholyan NV. Scaling behavior and structure of denatured proteins. Structure (London, England : 1993). 13: 1047-54. PMID 16004876 DOI: 10.1016/J.Str.2005.04.009  0.56
2005 Ding F, Guo W, Dokholyan NV, Shakhnovich EI, Shea JE. Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations. Journal of Molecular Biology. 350: 1035-50. PMID 15982666 DOI: 10.1016/J.Jmb.2005.05.017  0.667
2005 Ding F, Buldyrev SV, Dokholyan NV. Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model. Biophysical Journal. 88: 147-55. PMID 15533926 DOI: 10.1529/Biophysj.104.046375  0.57
2004 Dixon RD, Chen Y, Ding F, Khare SD, Prutzman KC, Schaller MD, Campbell SL, Dokholyan NV. New insights into FAK signaling and localization based on detection of a FAT domain folding intermediate. Structure (London, England : 1993). 12: 2161-71. PMID 15576030 DOI: 10.1016/J.Str.2004.09.011  0.694
2004 Khare SD, Caplow M, Dokholyan NV. The rate and equilibrium constants for a multistep reaction sequence for the aggregation of superoxide dismutase in amyotrophic lateral sclerosis. Proceedings of the National Academy of Sciences of the United States of America. 101: 15094-9. PMID 15475574 DOI: 10.1073/pnas.0406650101  0.452
2004 Urbanc B, Cruz L, Ding F, Sammond D, Khare S, Buldyrev SV, Stanley HE, Dokholyan NV. Molecular dynamics simulation of amyloid beta dimer formation. Biophysical Journal. 87: 2310-21. PMID 15454432 DOI: 10.1529/Biophysj.104.040980  0.703
2004 Tiana G, Dokholyan NV, Broglia RA, Shakhnovich EI. The evolution dynamics of model proteins. The Journal of Chemical Physics. 121: 2381-9. PMID 15260793 DOI: 10.1063/1.1768513  0.544
2004 Borreguero JM, Ding F, Buldyrev SV, Stanley HE, Dokholyan NV. Multiple folding pathways of the SH3 domain. Biophysical Journal. 87: 521-33. PMID 15240485 DOI: 10.1529/Biophysj.104.039529  0.795
2004 Peng S, Ding F, Urbanc B, Buldyrev SV, Cruz L, Stanley HE, Dokholyan NV. Discrete molecular dynamics simulations of peptide aggregation. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 69: 041908. PMID 15169044 DOI: 10.1103/Physreve.69.041908  0.672
2004 Khatun J, Khare SD, Dokholyan NV. Can contact potentials reliably predict stability of proteins? Journal of Molecular Biology. 336: 1223-38. PMID 15037081 DOI: 10.1016/j.jmb.2004.01.002  0.527
2004 Tiana G, Shakhnovich BE, Dokholyan NV, Shakhnovich EI. Imprint of evolution on protein structures. Proceedings of the National Academy of Sciences of the United States of America. 101: 2846-51. PMID 14970345 DOI: 10.1073/Pnas.0306638101  0.534
2003 Dokholyan NV, Borreguero JM, Buldyrev SV, Ding F, Stanley HE, Shakhnovich EI. Identifying importance of amino acids for protein folding from crystal structures. Methods in Enzymology. 374: 616-38. PMID 14696390 DOI: 10.1016/S0076-6879(03)74025-7  0.814
2003 Khare SD, Ding F, Dokholyan NV. Folding of Cu, Zn superoxide dismutase and familial amyotrophic lateral sclerosis. Journal of Molecular Biology. 334: 515-25. PMID 14623191 DOI: 10.1016/J.Jmb.2003.09.069  0.659
2003 Deeds EJ, Dokholyan NV, Shakhnovich EI. Protein evolution within a structural space. Biophysical Journal. 85: 2962-72. PMID 14581198 DOI: 10.1016/S0006-3495(03)74716-X  0.464
2003 Marqués MI, Borreguero JM, Stanley HE, Dokholyan NV. Possible mechanism for cold denaturation of proteins at high pressure. Physical Review Letters. 91: 138103. PMID 14525339 DOI: 10.1103/Physrevlett.91.138103  0.733
2003 Ding F, Borreguero JM, Buldyrey SV, Stanley HE, Dokholyan NV. Mechanism for the alpha-helix to beta-hairpin transition. Proteins. 53: 220-8. PMID 14517973 DOI: 10.1002/Prot.10468  0.774
2003 Pei J, Dokholyan NV, Shakhnovich EI, Grishin NV. Using protein design for homology detection and active site searches. Proceedings of the National Academy of Sciences of the United States of America. 100: 11361-6. PMID 12975528 DOI: 10.1073/Pnas.2034878100  0.44
2003 López E, Buldyrev SV, Dokholyan NV, Goldmakher L, Havlin S, King PR, Stanley HE. Postbreakthrough behavior in flow through porous media. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 67: 056314. PMID 12786279 DOI: 10.1103/Physreve.67.056314  0.568
2003 Shakhnovich BE, Dokholyan NV, DeLisi C, Shakhnovich EI. Functional fingerprints of folds: evidence for correlated structure-function evolution. Journal of Molecular Biology. 326: 1-9. PMID 12547186 DOI: 10.1016/S0022-2836(02)01362-1  0.448
2003 Buldyrev SV, Dokholyan NV, Erramilli S, Hong M, Kim JY, Malescio G, Stanley HE. Hierarchy in social organization Physica a: Statistical Mechanics and Its Applications. 330: 653-659. DOI: 10.1016/J.Physa.2003.09.041  0.4
2002 Ding F, Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich EI. Direct molecular dynamics observation of protein folding transition state ensemble. Biophysical Journal. 83: 3525-32. PMID 12496119 DOI: 10.1016/S0006-3495(02)75352-6  0.735
2002 Ding F, Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich EI. Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism. Journal of Molecular Biology. 324: 851-7. PMID 12460582 DOI: 10.1016/S0022-2836(02)01112-9  0.734
2002 Dokholyan NV, Shakhnovich B, Shakhnovich EI. Expanding protein universe and its origin from the biological Big Bang. Proceedings of the National Academy of Sciences of the United States of America. 99: 14132-6. PMID 12384571 DOI: 10.1073/Pnas.202497999  0.497
2002 Dokholyan NV, Li L, Ding F, Shakhnovich EI. Topological determinants of protein folding. Proceedings of the National Academy of Sciences of the United States of America. 99: 8637-41. PMID 12084924 DOI: 10.1073/Pnas.122076099  0.66
2002 Borreguero JM, Dokholyan NV, Buldyrev SV, Shakhnovich EI, Stanley HE. Thermodynamics and folding kinetics analysis of the SH3 domain form discrete molecular dynamics. Journal of Molecular Biology. 318: 863-76. PMID 12054829 DOI: 10.1016/S0022-2836(02)00136-5  0.805
2002 Dokholyan NV, Pitard E, Buldyrev SV, Stanley HE. Glassy behavior of a homopolymer from molecular dynamics simulations. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 65: 030801. PMID 11909019 DOI: 10.1103/Physreve.65.030801  0.443
2002 King PR, Buldyrev SV, Dokholyan NV, Havlin S, Lopez E, Paul G, Stanley HE. Using percolation theory to predict oil field performance Physica a: Statistical Mechanics and Its Applications. 314: 103-108. DOI: 10.1016/S0378-4371(02)01088-9  0.564
2002 Dokholyan NV, Mirny LA, Shakhnovich EI. Understanding conserved amino acids in proteins Physica a: Statistical Mechanics and Its Applications. 314: 600-606. DOI: 10.1016/S0378-4371(02)01079-8  0.468
2002 King PR, Buldyrev SV, Dokholyan NV, Havlin S, Lopez E, Paul G, Stanley HE. Uncertainty in oil production predicted by percolation theory Physica a: Statistical Mechanics and Its Applications. 306: 376-380. DOI: 10.1016/S0378-4371(02)00515-0  0.564
2001 Dokholyan NV, Shakhnovich EI. Understanding hierarchical protein evolution from first principles. Journal of Molecular Biology. 312: 289-307. PMID 11545603 DOI: 10.1006/Jmbi.2001.4949  0.51
2001 Scala A, Dokholyan NV, Buldyrev SV, Stanley HE. Thermodynamically important contacts in folding of model proteins. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 63: 032901. PMID 11308693 DOI: 10.1103/Physreve.63.032901  0.631
2001 King PR, Buldyrev SV, Dokholyan NV, Havlin S, Lee Y, Paul G, Stanley HE, Vandesteeg N. Predicting oil recovery using percolation theory Petroleum Geoscience. 7: S105-S107. DOI: 10.1144/Petgeo.7.S.S105  0.389
2000 Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich EI. Identifying the protein folding nucleus using molecular dynamics. Journal of Molecular Biology. 296: 1183-8. PMID 10698625 DOI: 10.1006/Jmbi.1999.3534  0.664
2000 Dokholyan NV, Buldyrev SV, Havlin S, Stanley HE. Distributions of dimeric tandem repeats in non-coding and coding DNA sequences. Journal of Theoretical Biology. 202: 273-82. PMID 10666360 DOI: 10.1006/Jtbi.1999.1052  0.409
1999 Lee Y, Andrade JS, Buldyrev SV, Dokholyan NV, Havlin S, King PR, Paul G, Stanley HE. Traveling time and traveling length in critical percolation clusters. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 60: 3425-8. PMID 11970164 DOI: 10.1103/Physreve.60.3425  0.387
1999 Stanley RH, Dokholyan NV, Buldyrev SV, Havlin S, Stanley HE. Clustering of identical oligomers in coding and noncoding DNA sequences. Journal of Biomolecular Structure & Dynamics. 17: 79-87. PMID 10496423 DOI: 10.1080/07391102.1999.10508342  0.385
1999 Buldyrev SV, Dokholyan NV, Havlin S, Stanley H, Stanley RH. Expansion of tandem repeats and oligomer clustering in coding and noncoding DNA sequences Physica a: Statistical Mechanics and Its Applications. 273: 19-32. DOI: 10.1016/S0378-4371(99)00338-6  0.393
1999 King P, Buldyrev S, Dokholyan N, Havlin S, Lee Y, Paul G, Stanley H. Applications of statistical physics to the oil industry: predicting oil recovery using percolation theory Physica a: Statistical Mechanics and Its Applications. 274: 60-66. DOI: 10.1016/S0378-4371(99)00327-1  0.393
1999 King PR, Jr. JS, Buldyrev SV, Dokholyan N, Lee Y, Havlin S, Stanley H. Predicting oil recovery using percolation Physica a: Statistical Mechanics and Its Applications. 266: 107-114. DOI: 10.1016/S0378-4371(98)00583-4  0.405
1999 Dokholyan NV, Buldyrev SV, Havlin S, King PR, Lee Y, Stanley H. Distribution of shortest paths in percolation Physica a: Statistical Mechanics and Its Applications. 266: 55-61. DOI: 10.1016/S0378-4371(98)00574-3  0.395
1998 Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich EI. Discrete molecular dynamics studies of the folding of a protein-like model. Folding & Design. 3: 577-87. PMID 9889167 DOI: 10.1016/S1359-0278(98)00072-8  0.644
1998 Dokholyan NV, Lee Y, Buldyrev SV, Havlin S, King PR, Stanley HE. Scaling of the Distribution of Shortest Paths in Percolation Journal of Statistical Physics. 93: 603-613. DOI: 10.1023/B:Joss.0000033244.13545.Da  0.394
1998 Dokholyan NV, Buldyrev SV, Havlin S, Stanley H. Model of unequal chromosomal crossing over in DNA sequences Physica a: Statistical Mechanics and Its Applications. 249: 594-599. DOI: 10.1016/S0378-4371(97)00520-7  0.416
1998 Buldyrev S, Dokholyan N, Goldberger A, Havlin S, Peng C, Stanley H, Viswanathan G. Analysis of DNA sequences using methods of statistical physics Physica a: Statistical Mechanics and Its Applications. 249: 430-438. DOI: 10.1016/S0378-4371(97)00503-7  0.415
1997 Dokholyan NV, Buldyrev SV, Havlin S, Stanley HE. Distribution of Base Pair Repeats in Coding and Noncoding DNA Sequences Physical Review Letters. 79: 5182-5185. DOI: 10.1103/Physrevlett.79.5182  0.408
Low-probability matches (unlikely to be authored by this person)
2019 Popov KI, Makepeace KAT, Petrotchenko EV, Dokholyan NV, Borchers CH. Insight into the Structure of the "Unstructured" Tau Protein. Structure (London, England : 1993). PMID 31628033 DOI: 10.1016/j.str.2019.09.003  0.294
2020 Zhang DY, Wang J, Dokholyan NV. Prefusion spike protein stabilization through computational mutagenesis. Proteins. PMID 33231324 DOI: 10.1002/prot.26025  0.289
2019 Makepeace KAT, Brodie NI, Popov KI, Gudavicius G, Nelson CJ, Petrotchenko EV, Dokholyan NV, Borchers CH. Ligand-induced disorder-to-order transitions characterized by structural proteomics and molecular dynamics simulations. Journal of Proteomics. 103544. PMID 31683063 DOI: 10.1016/j.jprot.2019.103544  0.283
2014 Kimura S, Caldarini M, Broglia RA, Dokholyan NV, Tiana G. The maturation of HIV-1 protease precursor studied by discrete molecular dynamics. Proteins. 82: 633-9. PMID 24123234 DOI: 10.1002/prot.24440  0.276
2006 Dokholyan NV. Studies of folding and misfolding using simplified models. Current Opinion in Structural Biology. 16: 79-85. PMID 16413773 DOI: 10.1016/j.sbi.2006.01.001  0.275
2015 Redler RL, Das J, Diaz JR, Dokholyan NV. Protein Destabilization as a Common Factor in Diverse Inherited Disorders. Journal of Molecular Evolution. PMID 26584803 DOI: 10.1007/s00239-015-9717-5  0.271
2005 Dokholyan NV. The architecture of the protein domain universe. Gene. 347: 199-206. PMID 15777630 DOI: 10.1016/j.gene.2004.12.020  0.268
2017 Zhu C, Mowrey DD, Dokholyan NV. Computational Protein Design Through Grafting and Stabilization. Methods in Molecular Biology (Clifton, N.J.). 1529: 227-241. PMID 27914054 DOI: 10.1007/978-1-4939-6637-0_11  0.268
2019 Brodie NI, Popov KI, Petrotchenko EV, Dokholyan NV, Borchers CH. Conformational ensemble of native α-synuclein in solution as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations. Plos Computational Biology. 15: e1006859. PMID 30917118 DOI: 10.1371/journal.pcbi.1006859  0.265
2023 Jain A, Dokholyan NV, Lee AL. Allosteric inactivation of an engineered optogenetic GTPase. Proceedings of the National Academy of Sciences of the United States of America. 120: e2219254120. PMID 36972433 DOI: 10.1073/pnas.2219254120  0.264
2010 Jha RK, Leaver-Fay A, Yin S, Wu Y, Butterfoss GL, Szyperski T, Dokholyan NV, Kuhlman B. Computational design of a PAK1 binding protein. Journal of Molecular Biology. 400: 257-70. PMID 20460129 DOI: 10.1016/J.Jmb.2010.05.006  0.264
2018 Li B, Tunc-Ozdemir M, Urano D, Jia H, Werth EG, Mowrey DD, Hicks LM, Dokholyan NV, Torres MP, Jones AM. Tyrosine phosphorylation switching of a G protein substrate. The Journal of Biological Chemistry. PMID 29382719 DOI: 10.1074/Jbc.Ra117.000163  0.26
2020 Dokholyan NV. Experimentally-driven protein structure modeling. Journal of Proteomics. 220: 103777. PMID 32268219 DOI: 10.1016/j.jprot.2020.103777  0.257
2021 Vishweshwaraiah YL, Chen J, Dokholyan NV. Engineering an Allosteric Control of Protein Function. The Journal of Physical Chemistry. B. PMID 33566608 DOI: 10.1021/acs.jpcb.0c11640  0.256
2022 Gomari MM, Tarighi P, Choupani E, Abkhiz S, Mohamadzadeh M, Rostami N, Sadroddiny E, Baammi S, Uversky VN, Dokholyan NV. Structural evolution of Delta lineage of SARS-CoV-2. International Journal of Biological Macromolecules. PMID 36435470 DOI: 10.1016/j.ijbiomac.2022.11.227  0.25
2002 Vendruscolo M, Dokholyan NV, Paci E, Karplus M. Small-world view of the amino acids that play a key role in protein folding. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 65: 061910. PMID 12188762 DOI: 10.1103/Physreve.65.061910  0.249
2004 Dokholyan NV. What is the protein design alphabet? Proteins. 54: 622-8. PMID 14997558 DOI: 10.1002/prot.10633  0.248
2021 Serpa JJ, Popov KI, Petrotchenko EV, Dokholyan NV, Borchers CH. Structure of prion β-oligomers as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations. Proteomics. e2000298. PMID 34482645 DOI: 10.1002/pmic.202000298  0.245
2022 Chen J, Vishweshwaraiah YL, Dokholyan NV. Design and engineering of allosteric communications in proteins. Current Opinion in Structural Biology. 73: 102334. PMID 35180676 DOI: 10.1016/j.sbi.2022.102334  0.242
2020 Wang J, Jain A, McDonald LR, Gambogi C, Lee AL, Dokholyan NV. Mapping allosteric communications within individual proteins. Nature Communications. 11: 3862. PMID 32737291 DOI: 10.1038/S41467-020-17618-2  0.241
2021 Vishweshwaraiah YL, Chen J, Chirasani VR, Tabdanov ED, Dokholyan NV. Two-input protein logic gate for computation in living cells. Nature Communications. 12: 6615. PMID 34785644 DOI: 10.1038/s41467-021-26937-x  0.241
2021 Chen J, Zaer S, Drori P, Zamel J, Joron K, Kalisman N, Lerner E, Dokholyan NV. The structural heterogeneity of α-synuclein is governed by several distinct subpopulations with interconversion times slower than milliseconds. Structure (London, England : 1993). PMID 34015255 DOI: 10.1016/j.str.2021.05.002  0.241
2017 Mu X, Choi S, Lang L, Mowray D, Dokholyan NV, Danielsson J, Oliveberg M. Physicochemical code for quinary protein interactions in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America. PMID 28536196 DOI: 10.1073/pnas.1621227114  0.24
2023 Godbole SS, Dokholyan NV. Allosteric regulation of kinase activity in living cells. Elife. 12. PMID 37943025 DOI: 10.7554/eLife.90574  0.231
2023 Godbole S, Dokholyan NV. Allosteric regulation of kinase activity in living cells. Biorxiv : the Preprint Server For Biology. PMID 37503033 DOI: 10.1101/2023.07.19.549709  0.231
2022 Agard DA, Bowman GR, DeGrado W, Dokholyan NV, Zhou HX. Solution of the protein structure prediction problem at last: crucial innovations and next frontiers. Faculty Reviews. 11: 38. PMID 36644294 DOI: 10.12703/r-01-0000020  0.225
2022 Binder JL, Berendzen J, Stevens AO, He Y, Wang J, Dokholyan NV, Oprea TI. AlphaFold illuminates half of the dark human proteins. Current Opinion in Structural Biology. 74: 102372. PMID 35439658 DOI: 10.1016/j.sbi.2022.102372  0.222
2017 Das J, Aleksandrov AA, Cui L, He L, Riordan JR, Dokholyan NV. Transmembrane helical interactions in the CFTR channel pore. Plos Computational Biology. 13: e1005594. PMID 28640808 DOI: 10.1371/journal.pcbi.1005594  0.213
2023 Chirasani VR, Khan MAI, Malavade JN, Dokholyan NV, Hoffman BD, Campbell SL. Molecular basis and cellular functions of vinculin-actin directional catch bonding. Nature Communications. 14: 8300. PMID 38097542 DOI: 10.1038/s41467-023-43779-x  0.211
2018 Zhang Y, Hashemi M, Lv Z, Williams B, Popov KI, Dokholyan NV, Lyubchenko YL. High-speed atomic force microscopy reveals structural dynamics of α-synuclein monomers and dimers. The Journal of Chemical Physics. 148: 123322. PMID 29604892 DOI: 10.1063/1.5008874  0.21
2020 Jiang H, Fan M, Wang J, Sarma A, Mohanty S, Dokholyan NV, Mahdavi M, Kandemir MT. Guiding Conventional Protein-Ligand Docking Software with Convolutional Neural Networks. Journal of Chemical Information and Modeling. 60: 4594-4602. PMID 33100014 DOI: 10.1021/acs.jcim.0c00542  0.208
2010 Yin S, Ding F, Dokholyan NV. Modeling Mutations in Proteins Using Medusa and Discrete Molecule Dynamics Introduction to Protein Structure Prediction: Methods and Algorithms. 453-476. DOI: 10.1002/9780470882207.ch20  0.207
2019 Reilley DJ, Popov K, Dokholyan NV, Alexandrova AN. Uncovered Dynamic Coupling Resolves the Ambiguous Mechanism of Phenylalanine Hydroxylase Oxygen Binding. The Journal of Physical Chemistry. B. PMID 31038957 DOI: 10.1021/Acs.Jpcb.9B02893  0.205
2023 Chen J, Vishweshwaraiah YL, Mailman RB, Tabdanov ED, Dokholyan NV. A noncommutative combinatorial protein logic circuit controls cell orientation in nanoenvironments. Science Advances. 9: eadg1062. PMID 37235645 DOI: 10.1126/sciadv.adg1062  0.204
2017 Kaur G, Guruprasad K, Temple BRS, Shirvanyants DG, Dokholyan NV, Pati PK. Structural complexity and functional diversity of plant NADPH oxidases. Amino Acids. PMID 29071531 DOI: 10.1007/s00726-017-2491-5  0.201
2018 Shobair M, Popov KI, Dang YL, He H, Stutts MJ, Dokholyan NV. Mapping allosteric linkage to channel gating of extracellular domains in the human epithelial sodium channel. The Journal of Biological Chemistry. PMID 29358325 DOI: 10.1074/jbc.RA117.000604  0.198
2022 Wang J, Dokholyan NV. Yuel: Improving the Generalizability of Structure-Free Compound-Protein Interaction Prediction. Journal of Chemical Information and Modeling. 62: 463-471. PMID 35103472 DOI: 10.1021/acs.jcim.1c01531  0.198
2023 Hnath B, Chen J, Reynolds J, Choi E, Wang J, Zhang D, Sha CM, Dokholyan NV. Big versus small: The impact of aggregate size in disease. Protein Science : a Publication of the Protein Society. e4686. PMID 37243896 DOI: 10.1002/pro.4686  0.197
2019 Zhu C, Dukhovlinova E, Council O, Ping L, Faison EM, Prabhu SS, Potter EL, Upton SL, Yin G, Fay JM, Kincer LP, Spielvogel E, Campbell SL, Benhabbour SR, Ke H, ... ... Dokholyan NV, et al. Rationally designed carbohydrate-occluded epitopes elicit HIV-1 Env-specific antibodies. Nature Communications. 10: 948. PMID 30814513 DOI: 10.1038/S41467-019-08876-W  0.197
2023 Chandrasekaran SN, Das J, Dokholyan NV, Carter CW. Microcalorimetry reveals multi-state thermal denaturation of tryptophanyl-tRNA synthetase. Structural Dynamics (Melville, N.Y.). 10: 044301. PMID 37476003 DOI: 10.1063/4.0000181  0.197
2021 Fan M, Wang J, Jiang H, Feng Y, Mahdavi M, Madduri K, Kandemir MT, Dokholyan NV. GPU-Accelerated Flexible Molecular Docking. The Journal of Physical Chemistry. B. PMID 33497567 DOI: 10.1021/acs.jpcb.0c09051  0.195
2022 Sha CM, Wang J, Dokholyan NV. NeuralDock: Rapid and Conformation-Agnostic Docking of Small Molecules. Frontiers in Molecular Biosciences. 9: 867241. PMID 35392534 DOI: 10.3389/fmolb.2022.867241  0.194
2016 Jacob RB, Michaels KC, Anderson CJ, Fay JM, Dokholyan NV. Harnessing Nature's Diversity: Discovering organophosphate bioscavenger characteristics among low molecular weight proteins. Scientific Reports. 6: 37175. PMID 27845442 DOI: 10.1038/srep37175  0.193
2009 Serohijos AWR, Hegedus T, Aleksandrov AA, He L, Cui L, Dokholyan NV, Riordan JR. Phenylalanine 508 Forms Intra-domain Contact Crucial To CFTR Folding And Dynamics Biophysical Journal. 96: 382a. DOI: 10.1016/j.bpj.2008.12.2857  0.192
2019 Wang J, Dokholyan NV. MedusaDock 2.0: Efficient and Accurate Protein-Ligand Docking With Constraints. Journal of Chemical Information and Modeling. PMID 30946779 DOI: 10.1021/acs.jcim.8b00905  0.192
2015 Allen SE, Dokholyan NV, Bowers AA. Dynamic docking of conformationally constrained macrocycles: methods and applications. Acs Chemical Biology. PMID 26575401 DOI: 10.1021/Acschembio.5B00663  0.192
2012 Dokholyan NV. Physical microscopic model of proteins under force. The Journal of Physical Chemistry. B. 116: 6806-9. PMID 22375559 DOI: 10.1021/jp212543m  0.192
2018 Cloer EW, Siesser PF, Cousins EM, Goldfarb D, Mowrey DD, Harrison JS, Weir SJ, Dokholyan NV, Major MB. p62-Dependent Phase Separation of Patient-Derived KEAP1 Mutations and NRF2. Molecular and Cellular Biology. 38. PMID 30126895 DOI: 10.1128/Mcb.00644-17  0.192
2023 Campbell S, Chirasani V, Khan M, Malavade J, Dokholyan N, Hoffman B. Elucidation of the Molecular Basis and Cellular Functions of Vinculin-Actin Directional Catch Bonding. Research Square. PMID 36711743 DOI: 10.21203/rs.3.rs-2334490/v1  0.191
2011 Shirvanyants D, Alexandrova AN, Dokholyan NV. Rigid substructure search Bioinformatics. 27: 1327-1329. PMID 21460026 DOI: 10.1093/Bioinformatics/Btr129  0.19
2017 Krokhotin A, Dokholyan NV. Protein folding: Over half a century lasting quest: Comment on "There and back again: Two views on the protein folding puzzle" by Alexei V. Finkelstein et al. Physics of Life Reviews. PMID 28599786 DOI: 10.1016/j.plrev.2017.06.002  0.19
2022 Hnath B, Dokholyan NV. Toxic SOD1 trimers are off-pathway in the formation of amyloid-like fibrils in ALS. Biophysical Journal. PMID 35505609 DOI: 10.1016/j.bpj.2022.04.037  0.187
2022 Vishweshwaraiah YL, Hnath B, Rackley B, Wang J, Gontu A, Chandler M, Afonin KA, Kuchipudi SV, Christensen N, Yennawar NH, Dokholyan NV. Adaptation-proof SARS-CoV-2 vaccine design. Advanced Functional Materials. 32. PMID 36590650 DOI: 10.1002/adfm.202206055  0.186
2022 Vishweshwaraiah YL, Hnath B, Rackley B, Wang J, Gontu A, Chandler M, Afonin KA, Kuchipudi SV, Christensen N, Yennawar NH, Dokholyan NV. Adaptation-proof SARS-CoV-2 vaccine design. Biorxiv : the Preprint Server For Biology. PMID 35611332 DOI: 10.1101/2022.05.17.492310  0.186
2023 Zamel J, Chen J, Zaer S, Harris PD, Drori P, Lebendiker M, Kalisman N, Dokholyan NV, Lerner E. Structural and dynamic insights into α-synuclein dimer conformations. Structure (London, England : 1993). PMID 36809765 DOI: 10.1016/j.str.2023.01.011  0.185
2021 Reilley DJ, Wang J, Dokholyan NV, Alexandrova AN. Titr-DMD-A Rapid, Coarse-Grained Quasi-All-Atom Constant pH Molecular Dynamics Framework. Journal of Chemical Theory and Computation. PMID 34165292 DOI: 10.1021/acs.jctc.1c00338  0.185
2019 Sapienza PJ, Popov K, Mowrey DD, Falk BT, Dokholyan NV, Lee AL. Inter-Active Site Communication Mediated by the Dimer Interface Beta-Sheet in the Half-the-Sites Enzyme, Thymidylate Synthase. Biochemistry. PMID 31283187 DOI: 10.1021/Acs.Biochem.9B00486  0.179
2008 Ozvegy-Laczka C, Laczkó R, Hegedus C, Litman T, Várady G, Goda K, Hegedus T, Dokholyan NV, Sorrentino BP, Váradi A, Sarkadi B. Interaction with the 5D3 monoclonal antibody is regulated by intramolecular rearrangements but not by covalent dimer formation of the human ABCG2 multidrug transporter. The Journal of Biological Chemistry. 283: 26059-70. PMID 18644784 DOI: 10.1074/Jbc.M803230200  0.179
2017 Dakal TC, Kala D, Dhiman G, Yadav V, Krokhotin A, Dokholyan NV. Predicting the functional consequences of non-synonymous single nucleotide polymorphisms in IL8 gene. Scientific Reports. 7: 6525. PMID 28747718 DOI: 10.1038/s41598-017-06575-4  0.177
2023 Sha CM, Wang J, Dokholyan NV. Differentiable rotamer sampling with molecular force fields. Briefings in Bioinformatics. 25. PMID 38095857 DOI: 10.1093/bib/bbad456  0.174
2017 Woods CT, Lackey L, Williams B, Dokholyan NV, Gotz D, Laederach A. Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo. Biophysical Journal. PMID 28625696 DOI: 10.1016/J.Bpj.2017.05.031  0.173
2023 Sha CM, Wang J, Dokholyan NV. Differentiable Rotamer Sampling with Molecular Force Fields. Arxiv. PMID 36866228  0.173
2012 Redler RL, Dokholyan NV. The complex molecular biology of amyotrophic lateral sclerosis (ALS). Progress in Molecular Biology and Translational Science. 107: 215-62. PMID 22482452 DOI: 10.1016/B978-0-12-385883-2.00002-3  0.17
2015 Brown KA, Zou Y, Shirvanyants D, Zhang J, Samanta S, Mantravadi PK, Dokholyan NV, Deiters A. Light-cleavable rapamycin dimer as an optical trigger for protein dimerization. Chemical Communications (Cambridge, England). 51: 5702-5. PMID 25716548 DOI: 10.1039/C4Cc09442E  0.17
2018 Zhu C, Beck MV, Griffith JD, Deshmukh M, Dokholyan NV. Large SOD1 aggregates, unlike trimeric SOD1, do not impact cell viability in a model of amyotrophic lateral sclerosis. Proceedings of the National Academy of Sciences of the United States of America. PMID 29666246 DOI: 10.1073/Pnas.1800187115  0.17
2021 Nguyen PH, Ramamoorthy A, Sahoo BR, Zheng J, Faller P, Straub JE, Dominguez L, Shea JE, Dokholyan NV, De Simone A, Ma B, Nussinov R, Najafi S, Ngo ST, Loquet A, et al. Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis. Chemical Reviews. PMID 33543942 DOI: 10.1021/acs.chemrev.0c01122  0.165
2008 Yin S, Biedermannova L, Vondrasek J, Dokholyan NV. MedusaScore: An accurate force field-based scoring function for virtual drug screening Journal of Chemical Information and Modeling. 48: 1656-1662. PMID 18672869 DOI: 10.1021/Ci8001167  0.165
2021 Vann KR, Vishweshwaraiah YL, Dokholyan NV, Kutateladze TG. Searching for methyllysine-binding aromatic cages. The Biochemical Journal. 478: 3613-3619. PMID 34624071 DOI: 10.1042/BCJ20210106  0.164
2017 Jacob RB, Michaels KC, Anderson CJ, Fay JM, Dokholyan NV. Corrigendum: Harnessing Nature's Diversity: Discovering organophosphate bioscavenger characteristics among low molecular weight proteins. Scientific Reports. 7: 46727. PMID 28452359 DOI: 10.1038/srep46727  0.164
2017 Jacob RB, Michaels KC, Anderson CJ, Fay JM, Dokholyan NV. Corrigendum: Harnessing Nature's Diversity: Discovering organophosphate bioscavenger characteristics among low molecular weight proteins. Scientific Reports. 7: 42832. PMID 28211477 DOI: 10.1038/srep42832  0.164
2021 Choi ES, Dokholyan NV. SOD1 oligomers in amyotrophic lateral sclerosis. Current Opinion in Structural Biology. 66: 225-230. PMID 33465527 DOI: 10.1016/j.sbi.2020.12.002  0.164
2019 Krokhotin A, Sarker M, Sevilla EA, Costantini LM, Griffith JD, Campbell SL, Dokholyan NV. Distinct Binding Modes of Vinculin Isoforms Underlie Their Functional Differences. Structure (London, England : 1993). PMID 31422909 DOI: 10.1016/J.Str.2019.07.013  0.162
2022 Gomari MM, Rostami N, Faradonbeh DR, Asemaneh HR, Esmailnia G, Arab S, Farsimadan M, Hosseini A, Dokholyan NV. Evaluation of pH change effects on the HSA folding and its drug binding characteristics, a computational biology investigation. Proteins. PMID 35569112 DOI: 10.1002/prot.26386  0.159
2017 Miao Z, Adamiak RW, Antczak M, Batey RT, Becka AJ, Biesiada M, Boniecki MJ, Bujnicki J, Chen SJ, Cheng CY, Chou FC, Ferré-D'Amaré AR, Das R, Dawson WK, Feng D, ... Dokholyan NV, et al. RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. Rna (New York, N.Y.). PMID 28138060 DOI: 10.1261/Rna.060368.116  0.159
2016 Chandrasekaran SN, Das J, Dokholyan NV, Carter CW. A modified PATH algorithm rapidly generates transition states comparable to those found by other well established algorithms. Structural Dynamics (Melville, N.Y.). 3: 012101. PMID 26958584 DOI: 10.1063/1.4941599  0.159
2019 Wodak SJ, Paci E, Dokholyan NV, Berezovsky IN, Horovitz A, Li J, Hilser VJ, Bahar I, Karanicolas J, Stock G, Hamm P, Stote RH, Eberhardt J, Chebaro Y, Dejaegere A, et al. Allostery in Its Many Disguises: From Theory to Applications. Structure (London, England : 1993). PMID 30744993 DOI: 10.1016/J.Str.2019.01.003  0.159
2013 Leonard CW, Hajdin CE, Karabiber F, Mathews DH, Favorov OV, Dokholyan NV, Weeks KM. Principles for understanding the accuracy of SHAPE-directed RNA structure modeling. Biochemistry. 52: 588-95. PMID 23316814 DOI: 10.1021/Bi300755U  0.158
2015 Krokhotin A, Dokholyan NV. Computational methods toward accurate RNA structure prediction using coarse-grained and all-atom models. Methods in Enzymology. 553: 65-89. PMID 25726461 DOI: 10.1016/bs.mie.2014.10.052  0.158
2023 Beasock D, Ha A, Halman J, Panigaj M, Wang J, Dokholyan NV, Afonin KA. Break to Build: Isothermal Assembly of Nucleic Acid Nanoparticles (NANPs) Enzymatic Degradation. Bioconjugate Chemistry. PMID 37293781 DOI: 10.1021/acs.bioconjchem.3c00167  0.157
2019 Krokhotin A, Du H, Hirabayashi K, Popov K, Kurokawa T, Wan X, Ferrone S, Dotti G, Dokholyan NV. Computationally Guided Design of Single-Chain Variable Fragment Improves Specificity of Chimeric Antigen Receptors. Molecular Therapy Oncolytics. 15: 30-37. PMID 31650023 DOI: 10.1016/J.Omto.2019.08.008  0.156
2019 Li X, Deng M, Petrucelli AS, Zhu C, Mo J, Zhang L, Tam JW, Ariel P, Zhao B, Zhang S, Ke H, Li P, Dokholyan NV, Duncan JA, Ting JP. Viral DNA Binding to NLRC3, an Inhibitory Nucleic Acid Sensor, Unleashes STING, a Cyclic Dinucleotide Receptor that Activates Type I Interferon. Immunity. 50: 591-599.e6. PMID 30893587 DOI: 10.1016/J.Immuni.2019.02.009  0.155
2012 Hsieh JH, Yin S, Wang XS, Liu S, Dokholyan NV, Tropsha A. Cheminformatics meets molecular mechanics: a combined application of knowledge-based pose scoring and physical force field-based hit scoring functions improves the accuracy of structure-based virtual screening. Journal of Chemical Information and Modeling. 52: 16-28. PMID 22017385 DOI: 10.1021/Ci2002507  0.154
2006 Petrotchenko EV, Pasek D, Elms P, Dokholyan NV, Meissner G, Borchers CH. Combining fluorescence detection and mass spectrometric analysis for comprehensive and quantitative analysis of redox-sensitive cysteines in native membrane proteins. Analytical Chemistry. 78: 7959-66. PMID 17134128 DOI: 10.1021/Ac060238R  0.154
2014 Redler RL, Fee L, Fay JM, Caplow M, Dokholyan NV. Non-native soluble oligomers of Cu/Zn superoxide dismutase (SOD1) contain a conformational epitope linked to cytotoxicity in amyotrophic lateral sclerosis (ALS). Biochemistry. 53: 2423-32. PMID 24660965 DOI: 10.1021/bi500158w  0.153
2010 Dokholyan NV. Multiscale Modeling and Design of Molecular Conformational States Biophysical Journal. 98: 633a. DOI: 10.1016/j.bpj.2009.12.3469  0.152
2015 Mei Y, Xu L, Mowrey DD, Mendez Giraldez R, Wang Y, Pasek DA, Dokholyan NV, Meissner G. Channel Gating Dependence on Pore Lining Helix Glycine Residues in Skeletal Muscle Ryanodine Receptor. The Journal of Biological Chemistry. 290: 17535-45. PMID 25998124 DOI: 10.1074/Jbc.M115.659672  0.149
2022 Miller WP, Sha CM, Sunilkumar S, Toro AL, VanCleave AM, Kimball SR, Dokholyan NV, Dennis MD. Activation of Disulfide Redox Switch in REDD1 Promotes Oxidative Stress Under Hyperglycemic Conditions. Diabetes. PMID 36170669 DOI: 10.2337/db22-0355  0.148
2014 Homan PJ, Favorov OV, Lavender CA, Kursun O, Ge X, Busan S, Dokholyan NV, Weeks KM. Single-molecule correlated chemical probing of RNA. Proceedings of the National Academy of Sciences of the United States of America. 111: 13858-63. PMID 25205807 DOI: 10.1073/Pnas.1407306111  0.147
2022 Chirasani VR, Wang J, Sha C, Raup-Konsavage W, Vrana K, Dokholyan NV. Whole proteome mapping of compound-protein interactions. Current Research in Chemical Biology. 2. PMID 38125869 DOI: 10.1016/j.crchbi.2022.100035  0.146
2022 Jiang H, Wang J, Cong W, Huang Y, Ramezani M, Sarma A, Dokholyan NV, Mahdavi M, Kandemir MT. Predicting Protein-Ligand Docking Structure with Graph Neural Network. Journal of Chemical Information and Modeling. PMID 35699430 DOI: 10.1021/acs.jcim.2c00127  0.146
2023 Sha CM, Wang J, Dokholyan NV. Predicting 3D RNA structure from the nucleotide sequence using Euclidean neural networks. Biophysical Journal. PMID 37838833 DOI: 10.1016/j.bpj.2023.10.011  0.144
2009 Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL, Fidelis K, Fiser A, Godzik A, Huang YJ, et al. Outcome of a workshop on applications of protein models in biomedical research. Structure (London, England : 1993). 17: 151-9. PMID 19217386 DOI: 10.1016/J.Str.2008.12.014  0.143
2011 Hsieh JH, Yin S, Liu S, Sedykh A, Dokholyan NV, Tropsha A. Combined application of cheminformatics- and physical force field-based scoring functions improves binding affinity prediction for CSAR data sets. Journal of Chemical Information and Modeling. 51: 2027-35. PMID 21780807 DOI: 10.1021/Ci200146E  0.142
2019 Wang J, Williams B, Chirasani VR, Krokhotin A, Das R, Dokholyan NV. Limits in accuracy and a strategy of RNA structure prediction using experimental information. Nucleic Acids Research. PMID 31106330 DOI: 10.1093/nar/gkz427  0.14
2019 Jiang Y, Zhang Y, Leung JY, Fan C, Popov KI, Su S, Qian J, Wang X, Holtzhausen A, Ubil E, Xiang Y, Davis I, Dokholyan NV, Wu G, Perou CM, et al. MERTK mediated novel site Akt phosphorylation alleviates SAV1 suppression. Nature Communications. 10: 1515. PMID 30944303 DOI: 10.1038/S41467-019-09233-7  0.139
2016 Krokhotin A, Mustoe AM, Weeks KM, Dokholyan NV. DIRECT IDENTIFICATION OF BASE-PAIRED RNA NUCLEOTIDES BY CORRELATED CHEMICAL PROBING. Rna (New York, N.Y.). PMID 27803152 DOI: 10.1261/Rna.058586.116  0.139
2017 Mowrey DD, Xu L, Mei Y, Pasek DA, Meissner G, Dokholyan NV. Ion-pulling simulations provide insights into the mechanisms of channel opening of the skeletal muscle ryanodine receptor. The Journal of Biological Chemistry. PMID 28584051 DOI: 10.1074/Jbc.M116.760199  0.135
2015 Krokhotin A, Houlihan K, Dokholyan NV. iFoldRNA v2: folding RNA with constraints. Bioinformatics (Oxford, England). 31: 2891-3. PMID 25910700 DOI: 10.1093/bioinformatics/btv221  0.131
2021 Zhovmer AS, Manning A, Smith C, Hayes JB, Burnette DT, Wang J, Cartagena-Rivera AX, Dokholyan NV, Singh RK, Tabdanov ED. Mechanical Counterbalance of Kinesin and Dynein Motors in a Microtubular Network Regulates Cell Mechanics, 3D Architecture, and Mechanosensing. Acs Nano. PMID 34677937 DOI: 10.1021/acsnano.1c04435  0.129
2021 Christy TW, Giannetti CA, Houlihan G, Smola MJ, Rice GM, Wang J, Dokholyan NV, Laederach A, Holliger P, Weeks KM. Direct Mapping of Higher-Order RNA Interactions by SHAPE-JuMP. Biochemistry. PMID 34121404 DOI: 10.1021/acs.biochem.1c00270  0.125
2024 Rebolledo LP, Ke W, Cedrone E, Wang J, Majithia K, Johnson MB, Dokholyan NV, Dobrovolskaia MA, Afonin KA. Immunostimulation of Fibrous Nucleic Acid Nanoparticles Can be Modulated through Aptamer-Based Functional Moieties: Unveiling the Structure-Activity Relationship and Mechanistic Insights. Acs Applied Materials & Interfaces. 16: 8430-8441. PMID 38344840 DOI: 10.1021/acsami.3c17779  0.125
2019 Sarker M, Lee HT, Mei L, Krokhotin A, de Los Reyes SE, Yen L, Costantini LM, Griffith J, Dokholyan NV, Alushin GM, Campbell SL. Cardiomyopathy Mutations in Metavinculin Disrupt Regulation of Vinculin-Induced F-Actin Assemblies. Journal of Molecular Biology. PMID 30844403 DOI: 10.1016/J.Jmb.2019.02.024  0.122
2007 Davis CH, Nie H, Dokholyan NV. Insights into thermophilic archaebacterial membrane stability from simplified models of lipid membranes. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 75: 051921. PMID 17677112 DOI: 10.1103/Physreve.75.051921  0.121
2022 Yang Y, Lewis MM, Huang X, Dokholyan NV, Mailman RB. Dopamine D receptor-mediated β-arrestin signaling: Insight from pharmacology, biology, behavior, and neurophysiology. The International Journal of Biochemistry & Cell Biology. 148: 106235. PMID 35688404 DOI: 10.1016/j.biocel.2022.106235  0.121
2014 Cholon DM, Quinney NL, Fulcher ML, Esther CR, Das J, Dokholyan NV, Randell SH, Boucher RC, Gentzsch M. Potentiator ivacaftor abrogates pharmacological correction of ΔF508 CFTR in cystic fibrosis. Science Translational Medicine. 6: 246ra96. PMID 25101886 DOI: 10.1126/Scitranslmed.3008680  0.121
2019 Chirasani VR, Xu L, Addis HG, Pasek DA, Dokholyan NV, Meissner G, Yamaguchi N. A central core disease mutation in the Ca binding site of skeletal muscle ryanodine receptor impairs single channel regulation. American Journal of Physiology. Cell Physiology. PMID 31166712 DOI: 10.1152/Ajpcell.00052.2019  0.12
2017 Xu L, Mowrey DD, Chirasani VR, Wang Y, Pasek DA, Dokholyan NV, Meissner G. G4941K substitution in the pore-lining S6 helix of the skeletal muscle ryanodine receptor increases RyR1 sensitivity to cytosolic and luminal Ca2. The Journal of Biological Chemistry. PMID 29255089 DOI: 10.1074/Jbc.M117.803247  0.12
2015 Shobair M, Dang YH, He H, Stutts JM, Dokholyan NV. W493R Gain of Function Mutation in Atypical Cystic Fibrosis Rewires the Epithelial Sodium Channel Dynamics Biophysical Journal. 108: 583a-584a. DOI: 10.1016/j.bpj.2014.11.3185  0.12
2020 Xu L, Harms FL, Chirasani VR, Pasek DA, Kortüm F, Meinecke P, Dokholyan NV, Kutsche K, Meissner G. Single-channel properties of skeletal muscle ryanodine receptor pore ΔFF in two brothers with a lethal form of fetal akinesia. Cell Calcium. 87: 102182. PMID 32097819 DOI: 10.1016/J.Ceca.2020.102182  0.12
2018 Ke W, Hong E, Saito RF, Rangel MC, Wang J, Viard M, Richardson M, Khisamutdinov EF, Panigaj M, Dokholyan NV, Chammas R, Dobrovolskaia MA, Afonin KA. RNA-DNA fibers and polygons with controlled immunorecognition activate RNAi, FRET and transcriptional regulation of NF-κB in human cells. Nucleic Acids Research. PMID 30517685 DOI: 10.1093/Nar/Gky1215  0.118
2021 Chirasani VR, Popov KI, Meissner G, Dokholyan NV. Mapping co-regulatory interactions among ligand-binding sites in ryanodine receptor 1. Proteins. PMID 34455637 DOI: 10.1002/prot.26228  0.117
2011 Yin S, Dokholyan NV. Fingerprint-based structure retrieval using electron density. Proteins. 79: 1002-9. PMID 21287628 DOI: 10.1002/prot.22941  0.115
2016 Gentzsch M, Ren HY, Houck SA, Quinney NL, Cholon DM, Sopha P, Chaudhry IG, Das J, Dokholyan NV, Randell SH, Cyr DM. Restoration of R117H CFTR Folding and Function in Human Airway Cells Through Combination Treatment with VX-809 and VX-770. American Journal of Physiology. Lung Cellular and Molecular Physiology. ajplung.00186.2016. PMID 27402691 DOI: 10.1152/ajplung.00186.2016  0.114
2021 Landoni E, Fucá G, Wang J, Chirasani VR, Yao Z, Dukhovlinova E, Ferrone S, Savoldo B, Hong LK, Shou P, Musio S, Padelli F, Finocchiaro G, Droste M, Kuhlman B, ... ... Dokholyan NV, et al. Modifications to the Framework Regions Eliminate Chimeric Antigen Receptor Tonic Signaling. Cancer Immunology Research. PMID 33547226 DOI: 10.1158/2326-6066.CIR-20-0451  0.112
2018 Xu L, Chirasani VR, Carter JS, Pasek DA, Dokholyan NV, Yamaguchi N, Meissner G. Ca2+-mediated activation of the skeletal-muscle ryanodine receptor ion channel. The Journal of Biological Chemistry. PMID 30341173 DOI: 10.1074/jbc.RA118.004453  0.11
2021 Chen YC, Dinavahi SS, Feng Q, Gowda R, Ramisetti S, Xia X, LaPenna KB, Chirasani VR, Cho SH, Hafenstein SL, Battu MB, Berg A, Sharma AK, Kirchhausen T, Dokholyan NV, et al. Activating sphingosine-1-phospahte signaling in endothelial cells increases myosin light chain phosphorylation to decrease endothelial permeability thereby inhibiting cancer metastasis. Cancer Letters. PMID 33600895 DOI: 10.1016/j.canlet.2021.01.004  0.109
2000 Andrade JS, Buldyrev SV, Dokholyan NV, Havlin S, King PR, Lee Y, Paul G, Eugene Stanley H. Flow between two sites on a percolation cluster Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 62: 8270-81. PMID 11138125 DOI: 10.1103/Physreve.62.8270  0.109
2023 Gomari MM, Arab SS, Balalaie S, Ramezanpour S, Hosseini A, Dokholyan NV, Tarighi P. Rational peptide design for targeting cancer cell invasion. Proteins. PMID 37646459 DOI: 10.1002/prot.26580  0.108
2023 Zhovmer AS, Manning A, Smith C, Wang J, Ma X, Tsygankov D, Dokholyan NV, Cartagena-Rivera AX, Singh RK, Tabdanov ED. Septins Enable T Cell Contact Guidance Amoeboid-Mesenchymal Switch. Biorxiv : the Preprint Server For Biology. PMID 37808814 DOI: 10.1101/2023.09.26.559597  0.106
2022 Gomari MM, Abkhiz S, Pour TG, Lotfi E, Rostami N, Monfared FN, Ghobari B, Mosavi M, Alipour B, Dokholyan NV. Peptidomimetics in cancer targeting. Molecular Medicine (Cambridge, Mass.). 28: 146. PMID 36476230 DOI: 10.1186/s10020-022-00577-3  0.106
2022 Tran AN, Chandler M, Halman J, Beasock D, Fessler A, McKeough RQ, Lam PA, Furr DP, Wang J, Cedrone E, Dobrovolskaia MA, Dokholyan NV, Trammell SR, Afonin KA. Anhydrous Nucleic Acid Nanoparticles for Storage and Handling at Broad Range of Temperatures. Small (Weinheim An Der Bergstrasse, Germany). e2104814. PMID 35128787 DOI: 10.1002/smll.202104814  0.102
2023 Wang J, Sha CM, Dokholyan NV. Combining Experimental Restraints and RNA 3D Structure Prediction in RNA Nanotechnology. Methods in Molecular Biology (Clifton, N.J.). 2709: 51-64. PMID 37572272 DOI: 10.1007/978-1-0716-3417-2_3  0.101
2020 Tyagi A, Chandrasekaran B, Kolluru V, Baby BV, Sripathi CA, Ankem MK, Ramisetti SR, Chirasani VR, Dokholyan NV, Sharma AK, Damodaran C. ASR490, a Small Molecule, Overrides Aberrant Expression of Notch1 in colorectal cancer. Molecular Cancer Therapeutics. PMID 33087513 DOI: 10.1158/1535-7163.MCT-19-0949  0.099
2022 Zhou S, Liu X, Fang X, Chinchilli VM, Wang M, Wang HG, Dokholyan NV, Shen C, Lee JJ. Robust and Efficient Assessment of Potency (REAP) as a quantitative tool for dose-response curve estimation. Elife. 11. PMID 35921131 DOI: 10.7554/eLife.78634  0.096
2019 Dinavahi SS, Gowda R, Gowda K, Bazewicz CG, Chirasani VR, Battu MB, Berg A, Dokholyan NV, Amin S, Robertson GP. Development of a novel multi-isoform ALDH inhibitor effective as an anti-melanoma agent. Molecular Cancer Therapeutics. PMID 31754071 DOI: 10.1158/1535-7163.Mct-19-0360  0.093
2012 Kotelnikova EA, Pyatnitskiy MA, Redler Rachel L. RL, Dokholyan NV. Role of Ca2+-Mediated signaling in als pathology From Knowledge Networks to Biological Models. 24-72. DOI: 10.2174/978160805437411201010024  0.091
2022 Ke W, Chandler M, Cedrone E, Saito RF, Rangel MC, de Souza Junqueira M, Wang J, Shi D, Truong N, Richardson M, Rolband LA, Dréau D, Bedocs P, Chammas R, Dokholyan NV, et al. Locking and Unlocking Thrombin Function Using Immunoquiescent Nucleic Acid Nanoparticles with Regulated Retention . Nano Letters. PMID 35786891 DOI: 10.1021/acs.nanolett.2c02019  0.088
2022 Vishweshwaraiah YL, Dokholyan NV. Toward rational vaccine engineering. Advanced Drug Delivery Reviews. 183: 114142. PMID 35150769 DOI: 10.1016/j.addr.2022.114142  0.085
2023 Chandrasekaran B, Tyagi A, Saran U, Kolluru V, Baby BV, Chirasani VR, Dokholyan NV, Lin JM, Singh A, Sharma AK, Ankem MK, Damodaran C. Urolithin A analog inhibits castration-resistant prostate cancer by targeting the androgen receptor and its variant, androgen receptor-variant 7. Frontiers in Pharmacology. 14: 1137783. PMID 36937838 DOI: 10.3389/fphar.2023.1137783  0.084
2018 Rackley L, Stewart JM, Salotti J, Krokhotin A, Shah A, Halman JR, Juneja R, Smollett J, Lee L, Roark K, Viard M, Tarannum M, Vivero-Escoto J, Johnson PF, Dobrovolskaia MA, ... Dokholyan NV, et al. RNA Fibers as Optimized Nanoscaffolds for siRNA Coordination and Reduced Immunological Recognition. Advanced Functional Materials. 28. PMID 31258458 DOI: 10.1002/Adfm.201805959  0.084
2022 Amorós MA, Choi ES, Cofré AR, Dokholyan NV, Duzzioni M. Motor neuron-derived induced pluripotent stem cells as a drug screening platform for amyotrophic lateral sclerosis. Frontiers in Cell and Developmental Biology. 10: 962881. PMID 36105357 DOI: 10.3389/fcell.2022.962881  0.08
2019 Chirasani VR, Xu L, Carter JS, Addis HG, Pasek DA, Dokholyan NV, Meissner G, Yamaguchi N. Mutation Analysis of the Calcium Binding Site of Skeletal Muscle Ryanodine Receptor Calcium Release Channel Biophysical Journal. 116: 520a-521a. DOI: 10.1016/J.Bpj.2018.11.2807  0.079
2022 Khazan N, Kim KK, Hansen JN, Singh NA, Moore T, Snyder CWA, Pandita R, Strawderman M, Fujihara M, Takamura Y, Jian Y, Battaglia N, Yano N, Teramoto Y, Arnold LA, ... ... Dokholyan NV, et al. Identification of a Vitamin-D Receptor Antagonist, MeTC7, which Inhibits the Growth of Xenograft and Transgenic Tumors . Journal of Medicinal Chemistry. PMID 35404047 DOI: 10.1021/acs.jmedchem.1c01878  0.079
2023 Raup-Konsavage WM, Sepulveda DE, Wang J, Dokholyan NV, Vrana KE, Graziane NM. Antinociceptive Effects of Cannabichromene (CBC) in Mice: Insights from von Frey, Tail-Flick, Formalin, and Acetone Tests. Biomedicines. 12. PMID 38255191 DOI: 10.3390/biomedicines12010083  0.078
2023 Sha CM, Wang J, Mailman RB, Yang Y, Dokholyan NV. Quantifying network behavior in the rat prefrontal cortex: a reproducibility crisis. Biorxiv : the Preprint Server For Biology. PMID 37292872 DOI: 10.1101/2023.05.16.541018  0.073
2018 Alva Sevilla E, Krokhotin A, Dokholyan NV. Vinculin and its Fundamental Role in Actin Bundling Formation Biophysical Journal. 114: 27a. DOI: 10.1016/j.bpj.2017.11.194  0.069
2020 Ono C, Fukuhara T, Li S, Wang J, Sato A, Izumi T, Fauzyah Y, Yamamoto T, Morioka Y, Dokholyan NV, Standley DM, Matsuura Y. Various miRNAs compensate the role of miR-122 on HCV replication. Plos Pathogens. 16: e1008308. PMID 32574204 DOI: 10.1371/journal.ppat.1008308  0.069
2020 Dokholyan NV. Molecular Design for Research and Therapeutics Biophysical Journal. 118: 42a. DOI: 10.1016/j.bpj.2019.11.412  0.066
2022 Dokholyan NV, Mohs RC, Bateman RJ. Challenges and progress in research, diagnostics, and therapeutics in Alzheimer's disease and related dementias. Alzheimer's & Dementia (New York, N. Y.). 8: e12330. PMID 35910674 DOI: 10.1002/trc2.12330  0.062
2023 Fang X, Liu X, Chinchilli VM, Wang M, Wang HG, Dokholyan NV, Shen C, Lee JJ, Zhou S. REAP-2: An interactive quantitative tool for robust and efficient dose-response curve estimation. Journal of Clinical and Translational Science. 7: e219. PMID 38028338 DOI: 10.1017/cts.2023.642  0.048
2022 Afonin KA, Dokholyan NV. Editorial to "Molecular engineering of biomaterials programmed to operate in living systems". Advanced Drug Delivery Reviews. 193: 114669. PMID 36529189 DOI: 10.1016/j.addr.2022.114669  0.048
2000 Paul G, Buldyrev SV, Dokholyan NV, Havlin S, King PR, Lee Y, Eugene Stanley H. Dependence of conductance on percolation backbone mass Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 61: 3435-40. PMID 11088120 DOI: 10.1103/Physreve.61.3435  0.04
2019 Campbell S, Sarker M, Lee HT, Kim L, de los Reyes SE, Mei L, Krokhotin A, Constantini L, Alushin GM, Dokholyan NV, Griffith JD. Coordinate Role of Vinculin and Metavinculin in Actin Organization Biophysical Journal. 116: 253a. DOI: 10.1016/J.Bpj.2018.11.1381  0.039
2023 Khazan N, Quarato ER, Singh NA, Snyder CWA, Moore T, Miller JP, Yasui M, Teramoto Y, Goto T, Reshi S, Hong J, Zhang N, Pandey D, Srivastava P, Morell A, ... ... Dokholyan NV, et al. Vitamin D Receptor Antagonist MeTC7 Inhibits PD-L1. Cancers. 15. PMID 37444542 DOI: 10.3390/cancers15133432  0.037
1998 Hong M, Jeung A, Dokholyan N, Smith T, Schwettman H, Huie P, Erramilli S. Imaging single living cells with a scanning near-field infrared microscope based on a free electron laser Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions With Materials and Atoms. 144: 246-255. DOI: 10.1016/S0168-583X(98)00311-5  0.032
2022 Vishweshwaraiah YL, Dokholyan NV. mRNA vaccines for cancer immunotherapy. Frontiers in Immunology. 13: 1029069. PMID 36591226 DOI: 10.3389/fimmu.2022.1029069  0.029
2021 Dokholyan NV. Nanoscale programming of cellular and physiological phenotypes: inorganic meets organic programming. Npj Systems Biology and Applications. 7: 15. PMID 33707429 DOI: 10.1038/s41540-021-00176-8  0.021
1994 Dokholyan N, Jikia G. Single top quark production and Vb CKM matrix element measurement in high energy e+e− collisions Physics Letters B. 336: 251-256. DOI: 10.1016/0370-2693(94)90244-5  0.021
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