Nikolay V. Dokholyan

发表

Gaia: automated quality assessment of protein structure models

Pradeep Kota, Feng Ding, Srinivas Ramachandran, 2011, Bioinform..

Thermodynamic Stability of Histone H3 Is a Necessary but not Sufficient Driving Force for its Evolutionary Conservation

Srinivas Ramachandran, Nikolay V. Dokholyan, Lisa Vogel, 2011, PLoS Comput. Biol..

Molecular Origin of Polyglutamine Aggregation in Neurodegenerative Diseases

Feng Ding, Nikolay V. Dokholyan, Sagar D. Khare, 2005, PLoS Comput. Biol..

F1000Prime recommendation of An investigation of the false discovery rate and the misinterpretation of p-values.

Nikolay V. Dokholyan, Elizabeth Anne Proctor, 2016 .

Identification and Rational Redesign of Peptide Ligands to CRIP1, A Novel Biomarker for Cancers

Nikolay V. Dokholyan, Jihua Hao, Adrian W. R. Serohijos, 2008, PLoS Comput. Biol..

Active Nuclear Receptors Exhibit Highly Correlated AF-2 Domain Motions

Feng Ding, Nikolay V. Dokholyan, Denise G. Teotico, 2008, PLoS Comput. Biol..

Rigid substructure search

Nikolay V. Dokholyan, Anastassia N. Alexandrova, David Shirvanyants, 2011, Bioinform..

Mapping allosteric communications within individual proteins

Nikolay V. Dokholyan, Jian Wang, Abha Jain, 2020, Nature Communications.

MedusaScore: An Accurate Force Field-Based Scoring Function for Virtual Drug Screening

Nikolay V. Dokholyan, Jirí Vondrásek, Shuangye Yin, 2008, J. Chem. Inf. Model..

Faculty Opinions recommendation of A fast mathematical programming procedure for simultaneous fitting of assembly components into cryoEM density maps.

Nikolay V. Dokholyan, Shuangye Yin, 2010 .

Transmembrane helical interactions in the CFTR channel pore

Nikolay V. Dokholyan, Liying Cui, Jhuma Das, 2017, PLoS Comput. Biol..

Knowledge-Based Models

Nikolay V. Dokholyan, Jhuma Das, Arpit Tandon, 2017 .

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

Nikolay V. Dokholyan, Konstantin Popov, Alexander Tropsha, 2016, J. Chem. Inf. Model..

A Structural Model of the Pore-Forming Region of the Skeletal Muscle Ryanodine Receptor (RyR1)

Srinivas Ramachandran, Nikolay V. Dokholyan, Adrian W. R. Serohijos, 2009, PLoS Comput. Biol..

Rapid Flexible Docking Using a Stochastic Rotamer Library of Ligands

Feng Ding, Nikolay V. Dokholyan, Shuangye Yin, 2010, J. Chem. Inf. Model..

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

Nikolay V. Dokholyan, Alexander Tropsha, Shubin Liu, 2012, J. Chem. Inf. Model..

iFold: a platform for interactive folding simulations of proteins

Feng Ding, Nikolay V. Dokholyan, Daniel Watson, 2006, Bioinform..

iFoldRNA v2: folding RNA with constraints

Nikolay V. Dokholyan, Andrey Krokhotin, Kevin Houlihan, 2015, Bioinform..

Combined Application of Cheminformatics- and Physical Force Field-Based Scoring Functions Improves Binding Affinity Prediction for CSAR Data Sets

Nikolay V. Dokholyan, Alexander Tropsha, Shubin Liu, 2011, J. Chem. Inf. Model..

iFoldRNA: three-dimensional RNA structure prediction and folding

Feng Ding, Nikolay V. Dokholyan, Shantanu Sharma, 2008, Bioinform..

F1000Prime recommendation of Allosteric Modulator Discovery: From Serendipity to Structure-Based Design.

Nikolay V. Dokholyan, 2019 .

Faculty Opinions recommendation of Principles for designing ideal protein structures.

Nikolay V. Dokholyan, David Shirvanyants, 2012 .

Polyglutamine Induced Misfolding of Huntingtin Exon1 is Modulated by the Flanking Sequences

Feng Ding, Nikolay V. Dokholyan, Vinal V. Lakhani, 2010, PLoS Comput. Biol..

Diminished Self-Chaperoning Activity of the ΔF508 Mutant of CFTR Results in Protein Misfolding

Nikolay V. Dokholyan, Adrian W. R. Serohijos, Tamás Hegedüs, 2008, PLoS Comput. Biol..

Molecular Design for Research and Therapeutics

Nikolay V. Dokholyan, 2020 .

Incorporating Backbone Flexibility in MedusaDock Improves Ligand-Binding Pose Prediction in the CSAR2011 Docking Benchmark

Feng Ding, Nikolay V. Dokholyan, F. Ding, 2013, J. Chem. Inf. Model..

Predicting Binding Affinity of CSAR Ligands Using Both Structure-Based and Ligand-Based Approaches

Feng Ding, Nikolay V. Dokholyan, Alexander Tropsha, 2013, J. Chem. Inf. Model..

Emergence of Protein Fold Families through Rational Design

Feng Ding, Nikolay V. Dokholyan, F. Ding, 2006, PLoS Comput. Biol..

ApoE4-specific Misfolded Intermediate Identified by Molecular Dynamics Simulations

Nikolay V. Dokholyan, Jhuma Das, Marino Convertino, 2015, PLoS Comput. Biol..

Drug Discovery Approaches using Quantum Machine Learning pdf

Nikolay V. Dokholyan, Swaroop Ghosh, Junde Li, 2021, ArXiv.

Invited: Drug Discovery Approaches using Quantum Machine Learning

Nikolay V. Dokholyan, Swaroop Ghosh, Junde Li, 2021, 2021 58th ACM/IEEE Design Automation Conference (DAC).

Predicting oil recovery using percolation theory

Nikolay V. Dokholyan, Sergey V. Buldyrev, Shlomo Havlin, 2001, Petroleum Geoscience.

Hierarchy in social organization

Nikolay V. Dokholyan, Sergey V. Buldyrev, Shyamsunder Erramilli, 2003 .

Structure modeling of RNA using sparse NMR constraints

Feng Ding, Nikolay V. Dokholyan, Arpit Tandon, 2017, Nucleic acids research.

MedusaScore: An Accurate Force Field-Based Scoring Function for Virtual Drug Screening.

Nikolay V. Dokholyan, Lada Biedermannová, Jiri Vondrasek, 2008 .

Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo

Nikolay V. Dokholyan, David Gotz, Alain Laederach, 2017, Biophysical journal.

Dynamical roles of metal ions and the disulfide bond in Cu, Zn superoxide dismutase folding and aggregation

Feng Ding, Nikolay V. Dokholyan, F. Ding, 2008, Proceedings of the National Academy of Sciences.

Uncertainty in oil production predicted by percolation theory

Nikolay V. Dokholyan, Sergey V. Buldyrev, Shlomo Havlin, 2002 .

Discrete Molecular Dynamics Can Predict Helical Prestructured Motifs in Disordered Proteins

Nikolay V. Dokholyan, Tamás Horváth, Tamás Hegedűs, 2014, PloS one.

Multiple Membrane-Cytoplasmic Domain Contacts in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Mediate Regulation of Channel Gating*

Nikolay V. Dokholyan, Adrian W. R. Serohijos, Andrei A. Aleksandrov, 2008, Journal of Biological Chemistry.

Imaging single living cells with a scanning near-field infrared microscope based on a free electron laser

Nikolay V. Dokholyan, Todd I. Smith, Philip Huie, 1998 .

Engineered allosteric activation of kinases in living cells

Pradeep Kota, Feng Ding, Nikolay V. Dokholyan, 2010, Nature Biotechnology.

Engineering extrinsic disorder to control protein activity in living cells

Nikolay V. Dokholyan, David Shirvanyants, Ilme Schlichting, 2016, Science.

Model of unequal chromosomal crossing over in DNA sequences 1 1 This work is supported by NIH-HGP.

Nikolay V. Dokholyan, Sergey V. Buldyrev, Shlomo Havlin, 1998 .

Rational coupled dynamics network manipulation rescues disease-relevant mutant cystic fibrosis transmembrane conductance regulator

Pradeep Kota, Nikolay V. Dokholyan, Andrei A. Aleksandrov, 2014, Chemical science.

Distribution of Base Pair Repeats in Coding and Noncoding DNA Sequences

Nikolay V. Dokholyan, Sergey V. Buldyrev, Shlomo Havlin, 1997 .

Expansion of tandem repeats and oligomer clustering in coding and noncoding DNA sequences

Nikolay V. Dokholyan, Sergey V. Buldyrev, Shlomo Havlin, 1999 .

Single-molecule correlated chemical probing of RNA

Nikolay V. Dokholyan, Oleg V. Favorov, Christopher A. Lavender, 2014, Proceedings of the National Academy of Sciences.

Nikolay V. Dokholyan, Ivo Grosse, Boris Podobnik, 2007 .

Engineered Allosteric Activation of Kinases in Living Cells

Pradeep Kota, Feng Ding, Nikolay V. Dokholyan, 2011 .