| Year |
Citation |
Score |
| 2024 |
Zhang DY, Wang J, Huang G, Langberg S, Ding F, Dokholyan NV. APOE regulates the transport of GM1. Biorxiv : the Preprint Server For Biology. PMID 38617316 DOI: 10.1101/2024.04.02.587789 |
0.568 |
|
| 2023 |
Zheng C, Wei Y, Zhang P, Xu L, Zhang Z, Lin K, Hou J, Lv X, Ding Y, Chiu Y, Jain A, Islam N, Malovannaya A, Wu Y, Ding F, et al. CRISPR/Cas9 screen uncovers functional translation of cryptic lncRNA-encoded open reading frames in human cancer. The Journal of Clinical Investigation. 133. PMID 36856111 DOI: 10.1172/JCI159940 |
0.354 |
|
| 2021 |
Saikia N, Yanez-Orozco IS, Qiu R, Hao P, Milikisiyants S, Ou E, Hamilton GL, Weninger KR, Smirnova TI, Sanabria H, Ding F. Integrative structural dynamics probing of the conformational heterogeneity in synaptosomal-associated protein 25. Cell Reports. Physical Science. 2. PMID 34888535 DOI: 10.1016/j.xcrp.2021.100616 |
0.309 |
|
| 2020 |
Chen P, Ding F, Cai R, Javed I, Yang W, Zhang Z, Li Y, Davis TP, Ke PC, Chen C. Amyloidosis Inhibition, a New Frontier of the Protein Corona. Nano Today. 35. PMID 32728376 DOI: 10.1016/J.Nantod.2020.100937 |
0.408 |
|
| 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 |
0.633 |
|
| 2020 |
Xing Y, Sun Y, Wang B, Ding F. Morphological Determinants of Carbon Nanomaterial-Induced Amyloid Peptide Self-Assembly. Frontiers in Chemistry. 8: 160. PMID 32211382 DOI: 10.3389/Fchem.2020.00160 |
0.307 |
|
| 2020 |
Sun Y, Ding F. Thermo- and pH-responsive fibrillization of squid suckerin A1H1 peptide. Nanoscale. PMID 32108838 DOI: 10.1039/C9Nr09271D |
0.319 |
|
| 2020 |
Nandakumar A, Xing Y, Aranha RR, Faridi A, Kakinen A, Javed I, Koppel K, Pilkington EH, Purcell AW, Davis TP, Faridi P, Ding F, Ke PC. Human Plasma Protein Corona of Aβ Amyloid and Its Impact on IAPP Cross-Seeding. Biomacromolecules. PMID 31909987 DOI: 10.1021/Acs.Biomac.9B01650 |
0.373 |
|
| 2020 |
Hamilton GL, Saikia N, Park J, Kubiak J, Seidel CA, Bowen ME, Ding F, Sanabria H. Interdomain Dynamics Underlie Function and Regulation of Postsynaptic Density Protein 95 Biophysical Journal. 118: 336a. DOI: 10.1016/J.Bpj.2019.11.1874 |
0.332 |
|
| 2020 |
Saikia N, Hamilton GL, Sanabria H, Bowen ME, Ding F. Dynamic Organization in the Supertertiary Structure of PDZ3-SH3-GuK Core Supramodule of PSD-95 Scaffold Protein Biophysical Journal. 118: 206a. DOI: 10.1016/J.Bpj.2019.11.1237 |
0.39 |
|
| 2019 |
Faridi A, Sun Y, Mortimer M, Aranha RR, Nandakumar A, Li Y, Javed I, Kakinen A, Fan Q, Purcell AW, Davis TP, Ding F, Faridi P, Ke PC. Graphene quantum dots rescue protein dysregulation of pancreatic β-cells exposed to human islet amyloid polypeptide. Nano Research. 12: 2827-2834. PMID 31695851 DOI: 10.1007/S12274-019-2520-7 |
0.388 |
|
| 2019 |
Kakinen A, Xing Y, Hegoda Arachchi ND, Javed I, Feng L, Faridi A, Douek AM, Sun Y, Kaslin J, Davis TP, Higgins MJ, Ding F, Ke PC. Single-molecular hetero-amyloidosis of human islet amyloid polypeptide. Nano Letters. PMID 31455083 DOI: 10.1021/Acs.Nanolett.9B02771 |
0.367 |
|
| 2019 |
Sun Y, Kakinen A, Zhang C, Yang Y, Faridi A, Davis TP, Cao W, Ke PC, Ding F. Amphiphilic surface chemistry of fullerenols is necessary for inhibiting the amyloid aggregation of alpha-synuclein NACore. Nanoscale. PMID 31188372 DOI: 10.1039/C9Nr02407G |
0.318 |
|
| 2019 |
Ke PC, Pilkington EH, Sun Y, Javed I, Kakinen A, Peng G, Ding F, Davis TP. Mitigation of Amyloidosis with Nanomaterials. Advanced Materials (Deerfield Beach, Fla.). e1901690. PMID 31183916 DOI: 10.1002/Adma.201901690 |
0.417 |
|
| 2019 |
Sun Y, Kakinen A, Xing Y, Faridi P, Nandakumar A, Purcell AW, Davis TP, Ke PC, Ding F. Amyloid Self-Assembly of hIAPP8-20 via the Accumulation of Helical Oligomers, α-Helix to β-Sheet Transition, and Formation of β-Barrel Intermediates. Small (Weinheim An Der Bergstrasse, Germany). e1805166. PMID 30908844 DOI: 10.1002/Smll.201805166 |
0.305 |
|
| 2019 |
Kakinen A, Sun Y, Javed I, Faridi A, Pilkington EH, Faridi P, Purcell AW, Zhou R, Ding F, Lin S, Chun Ke P, Davis TP. Physical and Toxicological Profiles of Human IAPP Amyloids and Plaques. Science Bulletin. 64: 26-35. PMID 30662791 DOI: 10.1016/J.Scib.2018.11.012 |
0.337 |
|
| 2019 |
Sun Y, Kakinen A, Xing Y, Faridi P, Nandakumar A, Purcell AW, Davis TP, Ke PC, Ding F. Peptide Self‐Assembly: Amyloid Self‐Assembly of hIAPP8‐20 via the Accumulation of Helical Oligomers, α‐Helix to β‐Sheet Transition, and Formation of β‐Barrel Intermediates (Small 18/2019) Small. 15: 1970093. DOI: 10.1002/Smll.201970093 |
0.301 |
|
| 2018 |
Wang B, Sun Y, Davis TP, Ke PC, Wu Y, Ding F. Understanding Effects of PAMAM Dendrimer Size and Surface Chemistry on Serum Protein Binding with Discrete Molecular Dynamics Simulations. Acs Sustainable Chemistry & Engineering. 6: 11704-11715. PMID 30881771 DOI: 10.1021/Acssuschemeng.8B01959 |
0.386 |
|
| 2018 |
Sun Y, Kakinen A, Xing Y, Pilkington EH, Davis TP, Ke PC, Ding F. Nucleation of β-rich oligomers and β-barrels in the early aggregation of human islet amyloid polypeptide. Biochimica Et Biophysica Acta. Molecular Basis of Disease. 1865: 434-444. PMID 30502402 DOI: 10.1016/J.Bbadis.2018.11.021 |
0.344 |
|
| 2018 |
Faridi A, Sun Y, Okazaki Y, Peng G, Gao J, Kakinen A, Faridi P, Zhao M, Javed I, Purcell AW, Davis TP, Lin S, Oda R, Ding F, Ke PC. Mitigating Human IAPP Amyloidogenesis In Vivo with Chiral Silica Nanoribbons. Small (Weinheim An Der Bergstrasse, Germany). e1802825. PMID 30369028 DOI: 10.1002/Smll.201802825 |
0.333 |
|
| 2018 |
Wang M, Sun Y, Cao X, Peng G, Javed I, Kakinen A, Davis TP, Lin S, Liu J, Ding F, Ke PC. Graphene quantum dots against human IAPP aggregation and toxicity in vivo. Nanoscale. PMID 30350837 DOI: 10.1039/C8Nr07180B |
0.305 |
|
| 2018 |
Kakinen A, Adamcik J, Wang B, Ge X, Mezzenga R, Davis TP, Ding F, Ke PC. Nanoscale inhibition of polymorphic and ambidextrous IAPP amyloid aggregation with small molecules. Nano Research. 11: 3636-3647. PMID 30275931 DOI: 10.1007/S12274-017-1930-7 |
0.308 |
|
| 2018 |
Yanez Orozco IS, Mindlin FA, Ma J, Wang B, Levesque B, Spencer M, Rezaei Adariani S, Hamilton G, Ding F, Bowen ME, Sanabria H. Identifying weak interdomain interactions that stabilize the supertertiary structure of the N-terminal tandem PDZ domains of PSD-95. Nature Communications. 9: 3724. PMID 30214057 DOI: 10.1038/S41467-018-06133-0 |
0.415 |
|
| 2018 |
Sun Y, Ge X, Xing Y, Wang B, Ding F. β-barrel Oligomers as Common Intermediates of Peptides Self-Assembling into Cross-β Aggregates. Scientific Reports. 8: 10353. PMID 29985420 DOI: 10.1038/S41598-018-28649-7 |
0.321 |
|
| 2018 |
Sun Y, Ding F, Ming D. Nonnative Energetic Frustrations in Protein Folding at Residual Level: A Simulation Study of Homologous Immunoglobulin-like -Sandwich Proteins. International Journal of Molecular Sciences. 19. PMID 29783701 DOI: 10.3390/Ijms19051515 |
0.462 |
|
| 2018 |
Pilkington EH, Gustafsson OJR, Xing Y, Hernandez-Fernaud J, Zampronio C, Kakinen A, Faridi A, Ding F, Wilson P, Ke PC, Davis TP. Profiling the Serum Protein Corona of Fibrillar Human Islet Amyloid Polypeptide. Acs Nano. PMID 29746093 DOI: 10.1021/Acsnano.8B02346 |
0.432 |
|
| 2018 |
Ge X, Sun Y, Ding F. Structures and dynamics of β-barrel oligomer intermediates of amyloid-beta16-22 aggregation. Biochimica Et Biophysica Acta. PMID 29550287 DOI: 10.1016/J.Bbamem.2018.03.011 |
0.37 |
|
| 2018 |
Ge X, Yang Y, Sun Y, Cao W, Ding F. Islet Amyloid Polypeptide Promotes Amyloid-beta Aggregation by Binding-induced Helix-unfolding of the Amyloidogenic Core. Acs Chemical Neuroscience. PMID 29378116 DOI: 10.1021/Acschemneuro.7B00396 |
0.347 |
|
| 2018 |
Jia Z, Li L, Peng Y, Ding F, Alexov E. The capricious electrostatic force: Revealing the signaling pathway in integrin α2-I domain Journal of Theoretical and Computational Chemistry. 17: 1840001. DOI: 10.1142/S0219633618400011 |
0.334 |
|
| 2018 |
Yanez Orozco IS, Ma J, Ding F, Bowen ME, Sanabria H. Transient Interactions in Multidomain Proteins Identified by FRET Biophysical Journal. 114: 565a. DOI: 10.1016/J.Bpj.2017.11.3089 |
0.36 |
|
| 2017 |
Wang B, Pilkington EH, Sun Y, Davis TP, Ke PC, Ding F. Modulating protein amyloid aggregation with nanomaterials. Environmental Science. Nano. 4: 1772-1783. PMID 29230295 DOI: 10.1039/C7En00436B |
0.335 |
|
| 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 |
0.656 |
|
| 2017 |
Xing Y, Pilkington EH, Wang M, Nowell CJ, Kakinen A, Sun Y, Wang B, Davis TP, Ding F, Ke PC. Lysophosphatidylcholine modulates the aggregation of human islet amyloid polypeptide. Physical Chemistry Chemical Physics : Pccp. PMID 29115353 DOI: 10.1039/C7Cp06670H |
0.351 |
|
| 2017 |
Javed I, Sun Y, Adamcik J, Wang B, Kakinen A, Pilkington EH, Ding F, Mezzenga R, Davis TP, Ke PC. Co-fibrillization of pathogenic and functional amyloid proteins with gold nanoparticles against amyloidogenesis. Biomacromolecules. PMID 29095600 DOI: 10.1021/Acs.Biomac.7B01359 |
0.331 |
|
| 2017 |
Sun Y, Wang B, Ge X, Ding F. Distinct oligomerization and fibrillization dynamics of amyloid core sequences of amyloid-beta and islet amyloid polypeptide. Physical Chemistry Chemical Physics : Pccp. PMID 29038815 DOI: 10.1039/C7Cp05695H |
0.315 |
|
| 2017 |
Pilkington EH, Lai M, Ge X, Stanley WJ, Wang B, Wang M, Kakinen A, Sani MA, Whittaker MR, Gurzov EN, Ding F, Quinn JF, Davis TP, Ke PC. Star Polymers Reduce IAPP Toxicity via Accelerated Amyloid Aggregation. Biomacromolecules. PMID 29035554 DOI: 10.1021/Acs.Biomac.7B01301 |
0.369 |
|
| 2017 |
Yang J, Wang B, You Y, Chang WJ, Tang K, Wang YC, Zhang W, Ding F, Gunasekaran S. Probing the modulated formation of gold nanoparticles-beta-lactoglobulin corona complexes and their applications. Nanoscale. PMID 28869274 DOI: 10.1039/C7Nr02999C |
0.385 |
|
| 2017 |
Ge X, Kakinen A, Gurzov EN, Yang W, Pang L, Pilkington EH, Govindan-Nedumpully P, Chen P, Separovic F, Davis TP, Ke PC, Ding F. Zinc-coordination and C-peptide complexation: a potential mechanism for the endogenous inhibition of IAPP aggregation. Chemical Communications (Cambridge, England). PMID 28745731 DOI: 10.1039/C7Cc04291D |
0.312 |
|
| 2017 |
Ke PC, Sani MA, Ding F, Kakinen A, Javed I, Separovic F, Davis TP, Mezzenga R. Implications of peptide assemblies in amyloid diseases. Chemical Society Reviews. PMID 28702523 DOI: 10.1039/C7Cs00372B |
0.384 |
|
| 2017 |
Geitner NK, Zhao W, Ding F, Chen W, Wiesner MR. Mechanistic Insights from Discrete Molecular Dynamics Simulations of Pesticide-Nanoparticle Interactions. Environmental Science & Technology. PMID 28686420 DOI: 10.1021/Acs.Est.7B01674 |
0.303 |
|
| 2017 |
Pilkington EH, Xing Y, Wang B, Kakinen A, Wang M, Davis TP, Ding F, Ke PC. Effects of Protein Corona on IAPP Amyloid Aggregation, Fibril Remodelling, and Cytotoxicity. Scientific Reports. 7: 2455. PMID 28550295 DOI: 10.1038/S41598-017-02597-0 |
0.43 |
|
| 2017 |
Wang B, Blin T, Käkinen A, Ge X, Pilkington EH, Quinn JF, Whittaker MR, Davis TP, Chun Ke P, Ding F. Brushed Polyethylene Glycol and Phosphorylcholine as Promising Grafting Agents against Protein Binding Biophysical Journal. 112: 350a. DOI: 10.1016/J.Bpj.2016.11.1899 |
0.3 |
|
| 2017 |
Kakinen A, Wang B, Ge X, Mezzenga R, Davis TP, Ding F, Chun Ke P. Mesoscopic Properties and Molecular Mechanisms of IAPP Amyloid Inhibition and Remodeling with Small Molecules Biophysical Journal. 112: 340a. DOI: 10.1016/J.Bpj.2016.11.1839 |
0.37 |
|
| 2016 |
Wang B, Blin T, Käkinen A, Ge X, Pilkington EH, Quinn JF, Whittaker MR, Davis TP, Ke PC, Ding F. Brushed polyethylene glycol and phosphorylcholine for grafting nanoparticles against protein binding. Polymer Chemistry. 7: 6875-6879. PMID 28348639 DOI: 10.1039/C6Py01480A |
0.3 |
|
| 2016 |
Ding F, Peng W. Biophysical evaluation of protein structural flexibility for ligand biorecognition in solid solution. Physical Chemistry Chemical Physics : Pccp. PMID 26869026 DOI: 10.1039/c5cp07385e |
0.302 |
|
| 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 |
0.791 |
|
| 2016 |
Gurzov EN, Wang B, Pilkington EH, Chen P, Kakinen A, Stanley WJ, Litwak SA, Hanssen EG, Davis TP, Ding F, Ke PC. Inhibition of hIAPP Amyloid Aggregation and Pancreatic β-Cell Toxicity by OH-Terminated PAMAM Dendrimer. Small (Weinheim An Der Bergstrasse, Germany). PMID 26808649 DOI: 10.1002/Smll.201502317 |
0.351 |
|
| 2016 |
Nedumpully-Govindan P, Kakinen A, Pilkington EH, Davis TP, Chun Ke P, Ding F. Stabilizing Off-pathway Oligomers by Polyphenol Nanoassemblies for IAPP Aggregation Inhibition. Scientific Reports. 6: 19463. PMID 26763863 DOI: 10.1038/Srep19463 |
0.375 |
|
| 2016 |
Wang B, Gurzov E, Chun Ke P, Ding F. Multiscale Modeling of Dendrimers for Biological Applications Biophysical Journal. 110: 546a. DOI: 10.1016/J.Bpj.2015.11.2919 |
0.394 |
|
| 2015 |
Radic S, Davis TP, Ke PC, Ding F. Contrasting effects of nanoparticle-protein attraction on amyloid aggregation. Rsc Advances. 5: 105498. PMID 26989481 DOI: 10.1039/C5Ra20182A |
0.385 |
|
| 2015 |
Nedumpully-Govindan P, Gurzov EN, Chen P, Pilkington EH, Stanley WJ, Litwak SA, Davis TP, Ke PC, Ding F. Graphene oxide inhibits hIAPP amyloid fibrillation and toxicity in insulin-producing NIT-1 cells. Physical Chemistry Chemical Physics : Pccp. PMID 26625841 DOI: 10.1039/C5Cp05924K |
0.331 |
|
| 2015 |
Nedumpully-Govindan P, Yang Y, Andorfer R, Cao W, Ding F. Promotion or Inhibition of IAPP Aggregation by Zinc Coordination Depends on Its Relative Concentration. Biochemistry. PMID 26603575 DOI: 10.1021/Acs.Biochem.5B00891 |
0.319 |
|
| 2015 |
Adamczyk L, Adkins JK, Agakishiev G, Aggarwal MM, Ahammed Z, Alekseev I, Alford J, Anson CD, Aparin A, Arkhipkin D, Aschenauer EC, Averichev GS, Banerjee A, Beavis DR, Bellwied R, ... ... Ding F, et al. Precision Measurement of the Longitudinal Double-Spin Asymmetry for Inclusive Jet Production in Polarized Proton Collisions at sqrt[s]=200 GeV. Physical Review Letters. 115: 092002. PMID 26371644 DOI: 10.1103/Physrevlett.115.092002 |
0.405 |
|
| 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 |
0.646 |
|
| 2015 |
Wang B, Seabrook SA, Nedumpully-Govindan P, Chen P, Yin H, Waddington L, Epa VC, Winkler DA, Kirby JK, Ding F, Ke PC. Thermostability and reversibility of silver nanoparticle-protein binding. Physical Chemistry Chemical Physics : Pccp. 17: 1728-39. PMID 25461673 DOI: 10.1039/C4Cp04996A |
0.368 |
|
| 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 |
0.655 |
|
| 2014 |
Radic S, Nedumpully-Govindan P, Chen R, Salonen E, Brown JM, Ke PC, Ding F. Effect of fullerenol surface chemistry on nanoparticle binding-induced protein misfolding. Nanoscale. 6: 8340-9. PMID 24934397 DOI: 10.1039/C4Nr01544D |
0.429 |
|
| 2014 |
Nedumpully-Govindan P, Li L, Alexov EG, Blenner MA, Ding F. Structural and energetic determinants of tyrosylprotein sulfotransferase sulfation specificity. Bioinformatics (Oxford, England). 30: 2302-9. PMID 24794930 DOI: 10.1093/Bioinformatics/Btu309 |
0.423 |
|
| 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 |
0.796 |
|
| 2014 |
Govindan PN, Ding F. Development of Efficient Energy Function for Protein-Small Molecule Interactions in Medusadock Biophysical Journal. 106: 4-9. DOI: 10.1016/J.Bpj.2013.11.2302 |
0.314 |
|
| 2013 |
Ding F, Radic S, Chen R, Chen P, Geitner NK, Brown JM, Ke PC. Direct observation of a single nanoparticle-ubiquitin corona formation. Nanoscale. 5: 9162-9. PMID 23921560 DOI: 10.1039/C3Nr02147E |
0.323 |
|
| 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 |
0.619 |
|
| 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 |
0.637 |
|
| 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 |
0.793 |
|
| 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 |
0.713 |
|
| 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 |
0.618 |
|
| 2013 |
Wen Y, Geitner NK, Chen R, Ding F, Chen P, Andorfer RE, Govindan PN, Ke PC. Binding of cytoskeletal proteins with silver nanoparticles Rsc Advances. 3: 22002-22007. DOI: 10.1039/C3Ra43281E |
0.307 |
|
| 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 |
0.67 |
|
| 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 |
0.677 |
|
| 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, 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 |
0.591 |
|
| 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 |
0.654 |
|
| 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 |
0.63 |
|
| 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 |
0.818 |
|
| 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 |
0.675 |
|
| 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 |
0.661 |
|
| 2012 |
Ding F, Dokholyan NV. Discrete Molecular Dynamics Simulation of Biomolecules Bulletin of the American Physical Society. 78: 55-73. DOI: 10.1007/978-1-4614-2146-7_3 |
0.348 |
|
| 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 |
0.792 |
|
| 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 |
0.783 |
|
| 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 |
0.811 |
|
| 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 |
0.752 |
|
| 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 |
0.823 |
|
| 2011 |
Proctor EA, Ding F, Dokholyan NV. Discrete molecular dynamics Wiley Interdisciplinary Reviews: Computational Molecular Science. 1: 80-92. DOI: 10.1002/Wcms.4 |
0.653 |
|
| 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 |
0.608 |
|
| 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 |
0.677 |
|
| 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 |
0.769 |
|
| 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 |
0.66 |
|
| 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 |
0.657 |
|
| 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 |
0.671 |
|
| 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 |
0.793 |
|
| 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 |
0.621 |
|
| 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 |
0.665 |
|
| 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 |
0.659 |
|
| 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 |
0.64 |
|
| 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 |
0.604 |
|
| 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 |
0.798 |
|
| 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 |
0.718 |
|
| 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 |
0.754 |
|
| 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 |
0.727 |
|
| 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 |
0.802 |
|
| 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 |
0.696 |
|
| 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 |
0.828 |
|
| 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 |
0.758 |
|
| 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 |
0.722 |
|
| 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 |
0.636 |
|
| 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 |
0.691 |
|
| 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 |
0.652 |
|
| 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 |
0.778 |
|
| 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 |
0.769 |
|
| 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 |
0.673 |
|
| 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 |
0.636 |
|
| 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 |
0.701 |
|
| 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 |
0.642 |
|
| 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 |
0.677 |
|
| 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 |
0.73 |
|
| 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 |
0.68 |
|
| 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 |
0.718 |
|
| 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 |
0.719 |
|
| 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 |
0.73 |
|
| 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 |
0.751 |
|
| 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 |
0.768 |
|
| 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 |
0.806 |
|
| 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 |
0.749 |
|
| 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 |
0.825 |
|
| 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 |
0.736 |
|
| 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 |
0.791 |
|
| 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 |
0.771 |
|
| 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 |
0.771 |
|
| 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 |
0.707 |
|
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