World's Best Scientists 2026 revealed!

D-Index & Metrics

Biology and Biochemistry

D-Index
88
Citations
25009
World Ranking
2731
National Ranking
1414

Research.com Recognitions

  • 2019 - Fellow of the American Association for the Advancement of Science (AAAS)
  • 2012 - Fellow of American Physical Society (APS) Citation For using multiscale modeling techniques to advance our understanding of physical interactions within and between biological molecules that yield insights into their complex organization, behavior, and evolution He has served the community by making his these tools publicly accessible

Overview

Nikolay V. Dokholyan is affiliated with Pennsylvania State University in the United States. Their research primarily focuses on the field of Biochemistry, Genetics and Molecular Biology, with a significant concentration in Molecular Biology.

The scientist's work spans several specialized subfields, including:

  • Molecular Biology
  • Neurology
  • Materials Chemistry
  • Cellular and Molecular Neuroscience
  • Computational Theory and Mathematics

Main topics addressed in their research include:

  • Protein Structure and Dynamics
  • RNA and protein synthesis mechanisms
  • Computational Drug Discovery Methods
  • Alzheimer's disease research and treatments
  • Parkinson's Disease Mechanisms and Treatments
  • RNA modifications and cancer
  • Amyotrophic Lateral Sclerosis Research

Dokholyan has published extensively, with notable venues for their work including UNC Libraries, bioRxiv (Cold Spring Harbor Laboratory), Faculty Opinions - Post-Publication Peer Review of the Biomedical Literature, Zenodo (CERN European Organization for Nuclear Research), and OPAL (Open@LaTrobe) (La Trobe University).

Frequent collaboration partners in their publications are:

  • Jian Wang
  • Feng Ding
  • Congzhou M. Sha
  • Jiaxing Chen
  • Yashavantha L. Vishweshwaraiah

Representative recent papers authored or co-authored by Dokholyan include:

  • Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis, 2021, Chemical Reviews
  • Mapping allosteric communications within individual proteins, 2020, Nature Communications
  • RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers, 2020, RNA
  • mRNA vaccines for cancer immunotherapy, 2022, Frontiers in Immunology
  • AlphaFold illuminates half of the dark human proteins, 2022, Current Opinion in Structural Biology

Dokholyan has been recognized with awards including Fellowship in the American Association for the Advancement of Science in 2019 and Fellowship in the American Physical Society in 2012. The APS fellowship citation notes their use of multiscale modeling techniques to explore physical interactions within and between biological molecules, as well as making these tools publicly accessible.

Best Publications

  • Automated minimization of steric clashes in protein structures.

    Srinivas Ramachandran;Pradeep Kota;Feng Ding;Nikolay V. Dokholyan

  • Amyloid oligomers: A joint experimental/computational perspective on Alzheimer's disease, Parkinson's disease, type II diabetes, and amyotrophic lateral sclerosis

    Phuong H. Nguyen;Ayyalusamy Ramamoorthy;Bikash R. Sahoo;Jie Zheng

  • Eris: an automated estimator of protein stability.

    Shuangye Yin;Feng Ding;Nikolay V Dokholyan

  • Small-world view of the amino acids that play a key role in protein folding.

    M. Vendruscolo;N. V. Dokholyan;E. Paci;M. Karplus

  • Phenylalanine-508 mediates a cytoplasmic–membrane domain contact in the CFTR 3D structure crucial to assembly and channel function

    Adrian W R Serohijos;Tamás Hegedus;Andrei A. Aleksandrov;Lihua He

  • Engineered Allosteric Activation of Kinases in Living Cells

    Andrei Karginov;Feng Ding;Pradeep Kota;Nikolay Dokholyan

  • Discrete molecular dynamics studies of the folding of a protein-like model.

    Nikolay V. Dokholyan;Sergey V. Buldyrev;H Eugene Stanley;Eugene I. Shakhnovich

  • Allostery in Its Many Disguises: From Theory to Applications

    Shoshana J. Wodak;Emanuele Paci;Nikolay V. Dokholyan;Nikolay V. Dokholyan;Igor N. Berezovsky

  • Topological determinants of protein folding

    Nikolay V. Dokholyan;Lewyn Li;Feng Ding;Eugene I. Shakhnovich

  • Ab Initio Folding of Proteins with All-Atom Discrete Molecular Dynamics

    Feng Ding;Douglas Tsao;Huifen Nie;Nikolay V. Dokholyan

  • Potentiator ivacaftor abrogates pharmacological correction of ΔF508 CFTR in cystic fibrosis

    Deborah M. Cholon;Nancy L. Quinney;M. Leslie Fulcher;Charles R. Esther

  • Mechanism for the α‐helix to β‐hairpin transition

    Feng Ding;Jose M. Borreguero;Sergey V. Buldyrey;H. Eugene Stanley

  • Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms

    Feng Ding;Shantanu Sharma;Poornima Chalasani;Vadim V. Demidov

  • Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008

    Mayako Michino;Enrique Abola;Charles L. Brooks;J. Scott Dixon

  • Controlling Allosteric Networks in Proteins.

    Nikolay V. Dokholyan

  • RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction

    José Almeida Cruz;Marc Frédérick Blanchet;Michal Boniecki;Janusz M. Bujnicki;Janusz M. Bujnicki

  • iFoldRNA: three-dimensional RNA structure prediction and folding

    Shantanu Sharma;Feng Ding;Nikolay V. Dokholyan

  • Molecular Dynamics Simulation of Amyloid β Dimer Formation

    B. Urbanc;L. Cruz;F. Ding;F. Ding;D. Sammond

  • The interface of protein structure, protein biophysics, and molecular evolution.

    David A Liberles;Sarah A Teichmann;Ivet Bahar;Ugo Bastolla

  • Engineering extrinsic disorder to control protein activity in living cells.

    Onur Dagliyan;Miroslaw Tarnawski;Pei Hsuan Chu;David Shirvanyants

Frequent Co-Authors

Feng Ding
Feng Ding Clemson University
Sergey V. Buldyrev
Sergey V. Buldyrev Yeshiva University
H. Eugene Stanley
H. Eugene Stanley Boston University
Eugene I. Shakhnovich
Eugene I. Shakhnovich Harvard University
Shlomo Havlin
Shlomo Havlin Bar-Ilan University
Luda Diatchenko
Luda Diatchenko McGill University
Gerhard Meissner
Gerhard Meissner University of North Carolina at Chapel Hill
John R. Riordan
John R. Riordan University of North Carolina at Chapel Hill
Kevin M. Weeks
Kevin M. Weeks University of North Carolina at Chapel Hill
Sharon L. Campbell
Sharon L. Campbell University of North Carolina at Chapel Hill

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