| Eris: an automated estimator of protein stability S Yin, F Ding, NV Dokholyan Nature methods 4 (6), 466-468, 2007 | 483 | 2007 |
| Automated minimization of steric clashes in protein structures S Ramachandran, P Kota, F Ding, NV Dokholyan Proteins: Structure, Function, and Bioinformatics 79 (1), 261-270, 2011 | 377 | 2011 |
| Ab initio folding of proteins with all-atom discrete molecular dynamics F Ding, D Tsao, H Nie, NV Dokholyan Structure 16 (7), 1010-1018, 2008 | 375 | 2008 |
| Mechanism for the α‐helix to β‐hairpin transition F Ding, JM Borreguero, SV Buldyrey, HE Stanley, NV Dokholyan Proteins: Structure, Function, and Bioinformatics 53 (2), 220-228, 2003 | 368* | 2003 |
| Topological determinants of protein folding NV Dokholyan, L Li, F Ding, EI Shakhnovich Proceedings of the National Academy of Sciences 99 (13), 8637-8641, 2002 | 366 | 2002 |
| Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment I Kufareva, M Rueda, V Katritch, G Dock, RC Stevens, R Abagyan Structure 19 (8), 1108-1126, 2011 | 349 | 2011 |
| Implications of peptide assemblies in amyloid diseases PC Ke, MA Sani, F Ding, A Kakinen, I Javed, F Separovic, TP Davis, ... Chemical Society Reviews 46 (21), 6492-6531, 2017 | 345 | 2017 |
| Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms F Ding, S Sharma, P Chalasani, VV Demidov, NE Broude, NV Dokholyan Rna 14 (6), 1164-1173, 2008 | 342 | 2008 |
| RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction JA Cruz, MF Blanchet, M Boniecki, JM Bujnicki, SJ Chen, S Cao, R Das, ... Rna 18 (4), 610-625, 2012 | 340 | 2012 |
| Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008 M Michino, E Abola, G Dock, CL Brooks III, JS Dixon, J Moult, RC Stevens Nature Reviews Drug Discovery 8 (6), 455, 2009 | 315 | 2009 |
| iFoldRNA: three-dimensional RNA structure prediction and folding S Sharma, F Ding, NV Dokholyan Bioinformatics 24 (17), 1951-1952, 2008 | 286 | 2008 |
| Molecular dynamics simulation of amyloid β dimer formation B Urbanc, L Cruz, F Ding, D Sammond, S Khare, SV Buldyrev, HE Stanley, ... Biophysical journal 87 (4), 2310-2321, 2004 | 260 | 2004 |
| Engineered allosteric activation of kinases in living cells AV Karginov, F Ding, P Kota, NV Dokholyan, KM Hahn Nature biotechnology 28 (7), 743, 2010 | 255 | 2010 |
| Emergence of protein fold families through rational design F Ding, NV Dokholyan PLoS Comput Biol 2 (7), e85, 2006 | 246 | 2006 |
| Chemical and biophysical signatures of the protein corona in nanomedicine J Ren, N Andrikopoulos, K Velonia, H Tang, R Cai, F Ding, PC Ke, ... Journal of the American Chemical Society 144 (21), 9184-9205, 2022 | 245 | 2022 |
| Discrete molecular dynamics: an efficient and versatile simulation method for fine protein characterization D Shirvanyants, F Ding, D Tsao, S Ramachandran, NV Dokholyan The journal of physical chemistry B 116 (29), 8375-8382, 2012 | 237 | 2012 |
| RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme Z Miao, RW Adamiak, M Antczak, RT Batey, AJ Becka, M Biesiada, ... RNA 23 (5), 655-672, 2017 | 219 | 2017 |
| RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures Z Miao, RW Adamiak, MF Blanchet, M Boniecki, JM Bujnicki, SJ Chen, ... Rna 21 (6), 1066-1084, 2015 | 216 | 2015 |
| Modeling backbone flexibility improves protein stability estimation S Yin, F Ding, NV Dokholyan Structure 15 (12), 1567-1576, 2007 | 200 | 2007 |
| Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism F Ding, NV Dokholyan, SV Buldyrev, HE Stanley, EI Shakhnovich Journal of molecular biology 324 (4), 851-857, 2002 | 200 | 2002 |
Nikolay DokholyanProfessorVerified email at virginia.edu
