Feng Ding, Ph.D. - Publications

Affiliations: 
Boston University, Boston, MA, United States 
Area:
Statistical physics

128 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

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  0.353
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  0.632
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  0.414
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  0.79
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  0.645
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  0.636
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  0.617
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  0.676
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  0.653
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  0.66
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  0.75
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  0.65
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  0.607
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  0.676
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  0.659
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  0.658
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  0.639
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  0.603
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  0.726
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  0.695
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  0.721
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  0.69
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  0.651
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  0.7
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  0.676
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  0.679
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  0.717
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  0.729
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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