Nikolay Dokholyan
Nikolay Dokholyan
G. Thomas Passananti Professor
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Amyloid oligomers: A joint experimental/computational perspective on Alzheimer’s disease, Parkinson’s disease, type II diabetes, and amyotrophic lateral sclerosis
PH Nguyen, A Ramamoorthy, BR Sahoo, J Zheng, P Faller, JE Straub, ...
Chemical reviews 121 (4), 2545-2647, 2021
Phenylalanine-508 mediates a cytoplasmic–membrane domain contact in the CFTR 3D structure crucial to assembly and channel function
AWR Serohijos, T Hegedűs, AA Aleksandrov, L He, L Cui, NV Dokholyan, ...
Proceedings of the National Academy of Sciences 105 (9), 3256-3261, 2008
Eris: an automated estimator of protein stability
S Yin, F Ding, NV Dokholyan
Nature methods 4 (6), 466-467, 2007
Small-world view of the amino acids that play a key role in protein folding
M Vendruscolo, NV Dokholyan, E Paci, M Karplus
Physical Review E 65 (6), 061910, 2002
Discrete molecular dynamics studies of the folding of a protein-like model
NV Dokholyan, SV Buldyrev, HE Stanley, EI Shakhnovich
Folding and design 3 (6), 577-587, 1998
Potentiator ivacaftor abrogates pharmacological correction of ΔF508 CFTR in cystic fibrosis
DM Cholon, NL Quinney, ML Fulcher, CR Esther Jr, J Das, NV Dokholyan, ...
Science translational medicine 6 (246), 246ra96-246ra96, 2014
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
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
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
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
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
Allostery in its many disguises: from theory to applications
SJ Wodak, E Paci, NV Dokholyan, IN Berezovsky, A Horovitz, J Li, ...
Structure 27 (4), 566-578, 2019
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
iFoldRNA: three-dimensional RNA structure prediction and folding
S Sharma, F Ding, NV Dokholyan
Bioinformatics 24 (17), 1951-1952, 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
The interface of protein structure, protein biophysics, and molecular evolution
DA Liberles, SA Teichmann, I Bahar, U Bastolla, J Bloom, ...
Protein Science 21 (6), 769-785, 2012
Emergence of protein fold families through rational design
F Ding, NV Dokholyan
PLoS computational biology 2 (7), e85, 2006
Analysis of DNA sequences using methods of statistical physics
SV Buldyrev, NV Dokholyan, AL Goldberger, S Havlin, CK Peng, ...
Physica A: Statistical Mechanics and its Applications 249 (1-4), 430-438, 1998
Controlling allosteric networks in proteins
NV Dokholyan
Chemical reviews 116 (11), 6463-6487, 2016
Engineered allosteric activation of kinases in living cells
AV Karginov, F Ding, P Kota, NV Dokholyan, KM Hahn
Nature biotechnology 28 (7), 743-747, 2010
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