N. Dokholyan

Eugene I Shakhnovich, Nikolay V Dokholyan, Boris E. Shakhnovich, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Drug Discovery Approaches using Quantum Machine Learning pdf

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

Ligand binding to a remote site thermodynamically corrects the F508del mutation in the human cystic fibrosis transmembrane conductance regulator

J. Riordan, B. Stockwell, N. Dokholyan, 2018, The Journal of Biological Chemistry.

RNA tertiary structure analysis by 2'-hydroxyl molecular interference.

K. Weeks, F. Ding, N. Dokholyan, 2014, Biochemistry.

Allostery in Its Many Disguises: From Theory to Applications.

Ruth Nussinov, Ivet Bahar, Dima Kozakov, 2019, Structure.

5 Towards Unifying Protein Evolution Theory

E. Shakhnovich, N. Dokholyan, 2007 .

Vinculin and its Fundamental Role in Actin Bundling Formation

N. Dokholyan, A. Krokhotin, Ernesto Alva Sevilla, 2018 .

Searching for methyllysine-binding aromatic cages.

N. Dokholyan, T. Kutateladze, Yashavantha L. Vishweshwaraiah, 2021, The Biochemical journal.

Interaction with the 5D3 Monoclonal Antibody Is Regulated by Intramolecular Rearrangements but Not by Covalent Dimer Formation of the Human ABCG2 Multidrug Transporter*

T. Litman, N. Dokholyan, G. Várady, 2008, Journal of Biological Chemistry.

AlphaFold illuminates half of the dark human proteins.

Tudor I. Oprea, Jessica L. Binder, T. Oprea, 2022, Current opinion in structural biology.

AlphaFold Models Illuminate Half of Dark Human Proteins

Tudor I. Oprea, Jessica L. Binder, T. Oprea, 2021 .

A central core disease mutation in the Ca2+ binding site of skeletal muscle ryanodine receptor impairs single channel regulation.

N. Dokholyan, G. Meissner, Le Xu, 2019, American journal of physiology. Cell physiology.

Fidelity of the protein structure reconstruction from inter-residue proximity constraints.

Feng Ding, Nikolay V Dokholyan, F. Ding, 2007, The journal of physical chemistry. B.

Engineered allosteric activation of kinases in living cells

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

ATP hydrolysis at one of the two sites in ABC transporters initiates transport related conformational transitions.

N. Dokholyan, S. Ramachandran, P. Kota, 2011, Biochimica et biophysica acta.

New insights into FAK signaling and localization based on detection of a FAT domain folding intermediate.

F. Ding, S. Khare, N. Dokholyan, 2004, Structure.

Discrete molecular dynamics: an efficient and versatile simulation method for fine protein characterization.

Feng Ding, Srinivas Ramachandran, David Shirvanyants, 2012, The journal of physical chemistry. B.

Outcome of a workshop on applications of protein models in biomedical research.

Roland L Dunbrack, Roland L. Dunbrack, Andrej Sali, 2009, Structure.

A Physical Model Reveals the Mechanochemistry Responsible for Dynein's Processive Motion

Adrian W. R. Serohijos, T. Elston, N. Dokholyan, 2022 .

Multiscale approaches for studying energy transduction in dynein.

Timothy C Elston, Shubin Liu, Adrian W. R. Serohijos, 2009, Physical chemistry chemical physics : PCCP.

Kinetic models for the coordinated stepping of cytoplasmic dynein.

Adrian W. R. Serohijos, T. Elston, N. Dokholyan, 2009, The Journal of chemical physics.

Modeling backbone flexibility improves protein stability estimation.

Feng Ding, Shuangye Yin, Nikolay V Dokholyan, 2007, Structure.

Molecular Origin of Polyglutamine Aggregation in Neurodegenerative Diseases

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

Isoform divergence of the filamin family of proteins.

N. Dokholyan, B. Temple, S. Milgram, 2010, Molecular biology and evolution.

Anhydrous Nucleic Acid Nanoparticles for Storage and Handling at Broad Range of Temperatures.

Riley Q. McKeough, Daniel P. Furr, Phuong Anh Lam, 2022, Small.

The path of DNA in the kinetochore

N. Dokholyan, K. Bloom, Shantanu Sharma, 2006, Current Biology.

The N-terminal Domain Allosterically Regulates Cleavage and Activation of the Epithelial Sodium Channel*

N. Dokholyan, P. Kota, M. Gentzsch, 2014, The Journal of Biological Chemistry.

Energetic and structural basis for activation of the epithelial sodium channel by matriptase.

N. Dokholyan, P. Kota, M. Gentzsch, 2012, Biochemistry.

Regulation of the epithelial Na+ channel and airway surface liquid volume by serine proteases

N. Dokholyan, P. Kota, M. Gentzsch, 2010, Pflügers Archiv - European Journal of Physiology.

Epithelial Sodium Channel Regulates Cleavage and Activation of the The N-terminal Domain Allosterically Molecular Biophysics

N. Dokholyan, P. Kota, M. Gentzsch, 2014 .

Mapping allosteric linkage to channel gating by extracellular domains in the human epithelial sodium channel

N. Dokholyan, K. Popov, M. Stutts, 2018, The Journal of Biological Chemistry.

Toxic SOD1 trimers are off-pathway in the formation of amyloid-like fibrils in ALS

N. Dokholyan, Brianna Hnath, 2021, bioRxiv.

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..

Prefusion spike protein stabilization through computational mutagenesis

N. Dokholyan, D. Zhang, Jian Wang, 2020, bioRxiv.

A Didactic Model of Macromolecular Crowding Effects on Protein Folding

N. Dokholyan, A. Minton, Douglas Tsao, 2010, PloS one.

The structural heterogeneity of α-synuclein is governed by several distinct subpopulations with interconversion times slower than milliseconds.

N. Dokholyan, Nir Kalisman, E. Lerner, 2021, Structure.

Redundant Functions for Nap1 and Chz1 in H2A.Z Deposition

Alexander T. Adams, B. Strahl, N. Dokholyan, 2017, Scientific Reports.

ApoE4-specific Misfolded Intermediate Identified by Molecular Dynamics Simulations

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

Approaches for probing the sequence space of substrates recognized by molecular chaperones.

N. Dokholyan, P. Kota, 2011, Methods.

Multiscale modeling of nucleosome dynamics.

Feng Ding, Nikolay V Dokholyan, Shantanu Sharma, 2007, Biophysical journal.

Direct Mapping of Higher-Order RNA Interactions by SHAPE-JuMP.

K. Weeks, A. Laederach, N. Dokholyan, 2021, Biochemistry.

Single-molecule correlated chemical probing of RNA

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

Rational design and implementation of a chemically inducible heterotrimerization system

T. Umehara, N. Dokholyan, Onur Dagliyan, 2020, Nature Methods.

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.

Regulator (abcc7) Structure Cystic Fibrosis Transmembrane Conductance Perspective the Cystic Fibrosis Gene: a Molecular Genetic Cystic Fibrosis Status of Fluid and Electrolyte Absorption in Phenotypes the Influence of Genetics on Cystic Fibrosis Assessing the Disease-liability of Mutations in Perspe

N. Dokholyan, J. Forman-Kay, P. Kota, 2022 .

Computational Modeling of Small Molecule Ligand Binding Interactions and Affinities.

Nikolay V Dokholyan, Marino Convertino, N. Dokholyan, 2016, Methods in molecular biology.

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..

Differences in the Antinociceptive Effects and Binding Properties of Propranolol and Bupranolol Enantiomers.

Nikolay V Dokholyan, Marino Convertino, William Maixner, 2015, The journal of pain : official journal of the American Pain Society.

Stabilization of μ‐opioid receptor facilitates its cellular translocation and signaling

Nikolay V Dokholyan, Marino Convertino, Cheng Zhu, 2019, Proteins.

Toward rational vaccine engineering.

N. Dokholyan, Yashavantha L. Vishweshwaraiah, 2022, Advanced drug delivery reviews.

Structure of prion β‐oligomers as determined by short‐distance crosslinking constraint‐guided discrete molecular dynamics simulations

N. Dokholyan, C. Borchers, Jason J. Serpa, 2021, Proteomics.

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

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

Flanking Bases Influence the Nature of DNA Distortion by Platinum 1,2-Intrastrand (GG) Cross-Links

Irene M. Baskerville-Abraham, N. Dokholyan, S. Ramachandran, 2011, PloS one.

Differences in Conformation and Conformational Dynamics Between Cisplatin and Oxaliplatin DNA Adducts

N. Dokholyan, S. Ramachandran, S. Chaney, 2009 .

Molecular dynamic simulations of cisplatin- and oxaliplatin-d(GG) intrastand cross-links reveal differences in their conformational dynamics.

N. Dokholyan, S. Chaney, Shantanu Sharma, 2007, Journal of molecular biology.

Deciphering protein dynamics from NMR data using explicit structure sampling and selection.

Nikolay V Dokholyan, N. Dokholyan, Yiwen Chen, 2007, Biophysical journal.

Intra- and Inter-Subunit Disulfide Bond Formation Is Nonessential in Adeno-Associated Viral Capsids

N. Dokholyan, P. Kota, A. Asokan, 2012, PloS one.

Tyrosine phosphorylation switching of a G protein

Alan M. Jones, N. Dokholyan, L. Hicks, 2018, The Journal of Biological Chemistry.

Ion Channels and Transporters in Lung Function and Disease Restoration of R 117 H CFTR folding and function in human airway cells through combination treatment with VX-809 and VX-770

N. Dokholyan, S. Randell, D. Cyr, 2016 .

Potentiator ivacaftor abrogates pharmacological correction of ΔF508 CFTR in cystic fibrosis

N. Dokholyan, S. Randell, M. Gentzsch, 2014, Science Translational Medicine.

Thermodynamic impacts of combinatorial mutagenesis on protein conformational stability: precise, high-throughput measurement by Thermofluor

C. Carter, N. Dokholyan, Jhuma Das, 2019, bioRxiv.

Computational approaches to understanding protein aggregation in neurodegeneration.

Pradeep Kota, Srinivas Ramachandran, Arpit Tandon, 2014, Journal of molecular cell biology.

Identification of an actin binding surface on vinculin that mediates mechanical cell and focal adhesion properties.

N. Dokholyan, R. Superfine, E. Egelman, 2014, Structure.

Molecular Mechanisms of the R61T Mutation in Apolipoprotein E4: A Dynamic Rescue.

N. Dokholyan, B. Williams, Jhuma Das, 2017, Biophysical journal.

Identification of novel integrin binding partners for calcium and integrin binding protein 1 (CIB1): structural and thermodynamic basis of CIB1 promiscuity.

Justin L. Black, Yi I. Wu, N. Dokholyan, 2013, Biochemistry.

Viral DNA Binding to NLRC3, an Inhibitory Nucleic Acid Sensor, Unleashes STING, a Cyclic Dinucleotide Receptor that Activates Type I Interferon

H. Ke, N. Dokholyan, Pablo Ariel, 2019, Immunity.

G Protein Mono-ubiquitination by the Rsp 5 Ubiquitin Ligase *

B. Kuhlman, H. Dohlman, Michael J. Lee, 2009 .

RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers

Feng Ding, Janusz M Bujnicki, Lin Huang, 2020, RNA.

Urolithin A analog inhibits castration-resistant prostate cancer by targeting the androgen receptor and its variant, androgen receptor-variant 7

N. Dokholyan, M. Ankem, C. Damodaran, 2023, Frontiers in Pharmacology.

Conformational ensemble of native α-synuclein in solution as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations

Christoph H Borchers, Nikolay V Dokholyan, Nicholas I Brodie, 2019, PLoS Comput. Biol..

High-speed atomic force microscopy reveals structural dynamics of α-synuclein monomers and dimers.

Y. Lyubchenko, N. Dokholyan, B. Williams, 2018, The Journal of chemical physics.

Structure modeling of RNA using sparse NMR constraints

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

Structural and functional interactions between six-transmembrane μ-opioid receptors and β2-adrenoreceptors modulate opioid signaling

B. Schmidt, E. Kalso, W. Maixner, 2015, Scientific Reports.

Local unfolding of Cu, Zn superoxide dismutase monomer determines the morphology of fibrillar aggregates.

F. Ding, N. Dokholyan, N. Nukina, 2012, Journal of molecular biology.

G4941K substitution in the pore-lining S6 helix of the skeletal muscle ryanodine receptor increases RyR1 sensitivity to cytosolic and luminal Ca2+

N. Dokholyan, D. Mowrey, G. Meissner, 2017, The Journal of Biological Chemistry.

Applications of Discrete Molecular Dynamics in biology and medicine.

Nikolay V Dokholyan, Elizabeth A Proctor, N. Dokholyan, 2016, Current opinion in structural biology.

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

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

MedusaDock 2.0: Efficient and Accurate Protein-Ligand Docking With Constraints

Jian Wang, Nikolay V Dokholyan, N. Dokholyan, 2019, J. Chem. Inf. Model..

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..

Computational evaluation of protein stability change upon mutations.

Feng Ding, Shuangye Yin, Nikolay V Dokholyan, 2010, Methods in molecular biology.

Gaia: automated quality assessment of protein structure models

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

Inter-Active Site Communication Mediated by the Dimer Interface Beta-Sheet in the Half-the-Sites Enzyme, Thymidylate Synthase.

Andrew L. Lee, N. Dokholyan, P. Sapienza, 2019, Biochemistry.

Rational design and implementation of a chemically inducible heterotrimerization system

T. Umehara, N. Dokholyan, Onur Dagliyan, 2020, Nature Methods.

GM1 mediates the formation and maintenance of cytotoxic Aβ oligomers

N. Dokholyan, E. Proctor, M. Swulius, 2021, bioRxiv.

RNA Three-Dimensional Structure Determination Using Experimental Constraints

F. Ding, N. Dokholyan, 2013 .

Computational design of chemogenetic and optogenetic split proteins

Alexander Deiters, Nikolay V Dokholyan, Onur Dagliyan, 2018, Nature Communications.

iFoldRNA: three-dimensional RNA structure prediction and folding

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

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

Feng Ding, Nikolay V. Dokholyan, Vinal V. Lakhani, 2010, 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..

Fast complementation of split fluorescent protein triggered by DNA hybridization

C. Cantor, F. Ding, N. Dokholyan, 2006, Proceedings of the National Academy of Sciences of the United States of America.

Computational design of chemogenetic and optogenetic split proteins

K. Hahn, N. Dokholyan, C. Der, 2018, Nature Communications.

Two-input protein logic gate for computation in living cells

N. Dokholyan, Yashavantha L. Vishweshwaraiah, V. Chirasani, 2021, Nature Communications.

Nanoscale programming of cellular and physiological phenotypes: inorganic meets organic programming

N. Dokholyan, 2021, npj Systems Biology and Applications.

Engineering an Allosteric Control of Protein Function.

N. Dokholyan, Yashavantha L. Vishweshwaraiah, Jiaxing Chen, 2021, The journal of physical chemistry. B.

Mapping allosteric communications within individual proteins

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

Engineering proteins for allosteric control by light or ligands

K. Hahn, N. Dokholyan, Onur Dagliyan, 2019, Nature Protocols.

Design and engineering of allosteric communications in proteins.

N. Dokholyan, Yashavantha L. Vishweshwaraiah, Jiaxing Chen, 2022, Current opinion in structural biology.

Yuel: Improving the Generalizability of Structure-Free Compound-Protein Interaction Prediction

N. Dokholyan, Jian Wang, 2022, J. Chem. Inf. Model..

Identification of a consensus motif in substrates bound by a Type I Hsp40

Pradeep Kota, Nikolay V Dokholyan, N. Dokholyan, 2009, Proceedings of the National Academy of Sciences.

Harnessing a Physiologic Mechanism for siRNA Delivery With Mimetic Lipoprotein Particles

Svetlana Shulga Morskaya, G. Wang, M. Stoffel, 2012, Molecular therapy : the journal of the American Society of Gene Therapy.

The rate and equilibrium constants for a multistep reaction sequence for the aggregation of superoxide dismutase in amyotrophic lateral sclerosis.

Nikolay V Dokholyan, Michael Caplow, Sagar D Khare, 2004, Proceedings of the National Academy of Sciences of the United States of America.

RNA–DNA fibers and polygons with controlled immunorecognition activate RNAi, FRET and transcriptional regulation of NF-κB in human cells

Emil F. Khisamutdinov, N. Dokholyan, M. Dobrovolskaia, 2018, Nucleic acids research.

Predicting Protein-Ligand Docking Structure with Graph Neural Network

Mahmut T. Kandemir, N. Dokholyan, Huaipan Jiang, 2022, J. Chem. Inf. Model..

A Phosphomimetic Mutation Stabilizes SOD1 and Rescues Cell Viability in the Context of an ALS-Associated Mutation.

H. Ke, N. Dokholyan, E. Proctor, 2016, Structure.

Natural selection against protein aggregation on self-interacting and essential proteins in yeast, fly, and worm.

Nikolay V Dokholyan, N. Dokholyan, Yiwen Chen, 2008, Molecular biology and evolution.

FALS mutations in Cu, Zn superoxide dismutase destabilize the dimer and increase dimer dissociation propensity: A large-scale thermodynamic analysis

Nikolay V Dokholyan, Michael Caplow, Sagar D Khare, 2006, Amyloid : the international journal of experimental and clinical investigation : the official journal of the International Society of Amyloidosis.

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.

Traffic within the cytochrome b6f lipoprotein complex: gating of the quinone portal.

N. Dokholyan, E. Yamashita, E. Proctor, 2014, Biophysical journal.

Non-native Soluble Oligomers of Cu/Zn Superoxide Dismutase (SOD1) Contain a Conformational Epitope Linked to Cytotoxicity in Amyotrophic Lateral Sclerosis (ALS)

N. Dokholyan, L. Fee, M. Caplow, 2014, Biochemistry.

Regioselectivity of Catechol O-Methyltransferase Confers Enhancement of Catalytic Activity.

N. Dokholyan, Shubin Liu, Douglas Tsao, 2011, Chemical physics letters.

Recognition of platinum-DNA adducts by HMGB1a.

N. Dokholyan, S. Ramachandran, S. Chaney, 2012, Biochemistry.

DNA sequence mediates nucleosome structure and stability.

N. Dokholyan, Shantanu Sharma, 2008, Biophysical journal.

Thermodynamics and folding kinetics analysis of the SH3 domain form discrete molecular dynamics.

H Eugene Stanley, Eugene I Shakhnovich, Nikolay V Dokholyan, 2002, Journal of molecular biology.

Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics.

Feng Ding, Kevin M Weeks, Nikolay V Dokholyan, 2009, Journal of the American Chemical Society.

Light regulation of protein dimerization and kinase activity in living cells using photocaged rapamycin and engineered FKBP.

K. Hahn, A. Karginov, N. Dokholyan, 2011, Journal of the American Chemical Society.

Rapid Flexible Docking Using a Stochastic Rotamer Library of Ligands

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

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..

Simple exponential acceleration of the power iteration algorithm pdf

Nikolay V Dokholyan, Congzhou M Sha, Congzhou M. Sha, 2021, ArXiv.

Cu,Zn-superoxide dismutase without Zn is folded but catalytically inactive.

N. Dokholyan, E. Proctor, R. Redler, 2014, Journal of molecular biology.

Title Cu , Zn-Superoxide Dismutase without Zn Is Folded but Catalytically Inactive Permalink

N. Dokholyan, E. Proctor, A. Alexandrova, 2014 .

Development of a Novel Multi-Isoform ALDH Inhibitor Effective as an Antimelanoma Agent

N. Dokholyan, G. Robertson, S. Amin, 2019, Molecular Cancer Therapeutics.

The maturation of HIV‐1 protease precursor studied by discrete molecular dynamics

R. Broglia, G. Tiana, N. Dokholyan, 2014, Proteins.

Ju n 20 03 1 Folding of Cu , Zn superoxide dismutase and Familial Amyotrophic Lateral Sclerosis

F. Ding, S. Khare, N. Dokholyan, 2008 .

Studies of folding and misfolding using simplified models.

Nikolay V Dokholyan, N. Dokholyan, 2006, Current opinion in structural biology.

Folding of Cu, Zn superoxide dismutase and familial amyotrophic lateral sclerosis.

Feng Ding, Nikolay V Dokholyan, Sagar D Khare, 2003, Journal of molecular biology.

Combining fluorescence detection and mass spectrometric analysis for comprehensive and quantitative analysis of redox-sensitive cysteines in native membrane proteins.

N. Dokholyan, C. Borchers, E. Petrotchenko, 2006, Analytical chemistry.

Computational studies reveal phosphorylation-dependent changes in the unstructured R domain of CFTR.

Adrian W. R. Serohijos, Nikolay V Dokholyan, Lihua He, 2008, Journal of molecular biology.

Experimentally-driven protein structure modeling.

Nikolay V Dokholyan, N. Dokholyan, 2020, Journal of proteomics.

Engineering Pak1 Allosteric Switches.

Haruo Kasai, Sho Yagishita, Hui Wang, 2017, ACS synthetic biology.

Dynamic Docking of Conformationally Constrained Macrocycles: Methods and Applications.

Nikolay V Dokholyan, Albert A Bowers, N. Dokholyan, 2016, ACS chemical biology.

Intrinsic disorder mediates cooperative signal transduction in STIM1.

K. Namba, S. Akira, T. Ikegami, 2014, Journal of Molecular Biology.

Engineering Pak 1 Allosteric Switches

Sho Yagishita, H. Kasai, K. Hahn, 2017 .

Structural and thermodynamic effects of post-translational modifications in mutant and wild type Cu, Zn superoxide dismutase.

F. Ding, N. Dokholyan, E. Proctor, 2011, Journal of molecular biology.

Break to Build: Isothermal Assembly of Nucleic Acid Nanoparticles (NANPs) via Enzymatic Degradation

N. Dokholyan, K. Afonin, J. Halman, 2023, Bioconjugate chemistry.

iFoldRNA v2: folding RNA with constraints

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

Mapping co‐regulatory interactions among ligand‐binding sites in ryanodine receptor 1

N. Dokholyan, G. Meissner, K. Popov, 2021, Proteins.

MERTK mediated novel site Akt phosphorylation alleviates SAV1 suppression

C. Fan, C. Perou, N. Dokholyan, 2019, Nature Communications.

Identification of a Vitamin-D Receptor Antagonist, MeTC7, which Inhibits the Growth of Xenograft and Transgenic Tumors In Vivo

Richard G. Moore, P. Jurutka, N. Dokholyan, 2022, Journal of medicinal chemistry.

Correction: Emergence of Protein Fold Families through Rational Design

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

Identification of post-transcriptional modifications in nucleic acid sequences using purpose-designed molecular beacons

James Ze Wang, Jennifer C. Jones, N. Dokholyan, 2023, bioRxiv.

A noncommutative combinatorial protein logic circuit controls cell orientation in nanoenvironments

R. Mailman, N. Dokholyan, Yashavantha L. Vishweshwaraiah, 2023, Science advances.

ASR490, a Small Molecule, Overrides Aberrant Expression of Notch1 in Colorectal Cancer

N. Dokholyan, M. Ankem, C. Damodaran, 2020, Molecular Cancer Therapeutics.

Discrete Molecular Dynamics Distinguishes Nativelike Binding Poses from Decoys in Difficult Targets

Alexander Tropsha, Shuangye Yin, Nikolay V Dokholyan, 2022 .

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..

Mapping Co-regulation Pathways among Ligand Binding sites in RyR1

N. Dokholyan, G. Meissner, K. Popov, 2019, bioRxiv.

Ca2+-mediated activation of the skeletal-muscle ryanodine receptor ion channel

N. Dokholyan, G. Meissner, Le Xu, 2018, The Journal of Biological Chemistry.

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

Dopamine D1 receptor-mediated β-arrestin signaling: Insight from pharmacology, biology, behavior, and neurophysiology.

R. Mailman, Xuemei Huang, N. Dokholyan, 2022, The international journal of biochemistry & cell biology.

N‐terminal strands of filamin Ig domains act as a conformational switch under biological forces

F. Ding, N. Dokholyan, B. Temple, 2010, Proteins.

Postbreakthrough behavior in flow through porous media.

H. Stanley, S. Havlin, S. Buldyrev, 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

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..

Molecular Dynamics Simulation of Amyloid b Dimer Formation

H. Stanley, S. Buldyrev, B. Urbanc, 2004 .

A Structural Model for Vinculin Insertion into PIP2-Containing Membranes and the Effect of Insertion on Vinculin Activation and Localization.

N. Dokholyan, S. Ramachandran, Arpit Tandon, 2017, Structure.

A Structural Model for Vinculin Insertion into PIP 2-ContainingMembranes and the Effect of Insertion on Vinculin Activation and Localization Graphical Abstract Highlights

N. Dokholyan, S. Ramachandran, Arpit Tandon, 2017 .

A Structural Model for Vin culin Insertion into PIP 2-ContainingMembranes and the Effect of Insertion on Vinculin Activation and Localization Graphical

N. Dokholyan, S. Ramachandran, Arpit Tandon, 2016 .

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..

Erratum: Correctors of dF508 CFTR restore global conformational maturation without thermally stabilizing the mutant protein (FASEB Journal (2013) 27 (536 -545) DOI:10.1096/fj.12-216119)

J. Riordan, N. Dokholyan, P. Kota, 2014 .

Toxic SOD1 trimers are off-pathway in the formation of amyloid-like fibrils in ALS.

N. Dokholyan, Brianna Hnath, 2022, Biophysical Journal.

Nonnative SOD1 trimer is toxic to motor neurons in a model of amyotrophic lateral sclerosis

Y. Lyubchenko, N. Dokholyan, E. Proctor, 2015, Proceedings of the National Academy of Sciences.

Titr-DMD-A Rapid, Coarse-Grained Quasi-All-Atom Constant pH Molecular Dynamics Framework.

N. Dokholyan, A. Alexandrova, David J. Reilley, 2021, Journal of chemical theory and computation.

Kinetics of the protein folding transition

H. Stanley, E. Shakhnovich, S. Buldyrev, 2001 .

Protein Destabilization as a Common Factor in Diverse Inherited Disorders

N. Dokholyan, R. Redler, Jhuma Das, 2015, Journal of Molecular Evolution.

Corrigendum: Harnessing Nature’s Diversity: Discovering organophosphate bioscavenger characteristics among low molecular weight proteins

Reed B. Jacob, Kenan C. Michaels, N. Dokholyan, 2017, Scientific Reports.

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

Feng Ding, Jian Wang, Janusz M Bujnicki, 2015, RNA.

BiPS, a Photocleavable, Isotopically Coded, Fluorescent Cross-linker for Structural Proteomics *

Christoph H Borchers, Nikolay V Dokholyan, Kunhong Xiao, 2009, Molecular & Cellular Proteomics.

Transmembrane helical interactions in the CFTR channel pore

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

Big versus small: The impact of aggregate size in disease

Congzhou M. Sha, N. Dokholyan, Jiaxing Chen, 2023, Protein science : a publication of the Protein Society.

β-Methylamino-L-alanine substitution of serine in SOD1 suggests a direct role in ALS etiology

Nikolay V Dokholyan, Elizabeth A Proctor, David D Mowrey, 2019, PLoS Comput. Biol..

Hybrid dynamics simulation engine for metalloproteins.

Feng Ding, Anastassia N Alexandrova, David Shirvanyants, 2012, Biophysical journal.

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 .

Rationally designed carbohydrate-occluded epitopes elicit HIV-1 Env-specific antibodies

S. L. Upton, E. L. Potter, Shamit S. Prabhu, 2019, Nature Communications.

Rigid substructure search

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

Allosteric regulation of kinase activity in living cells

N. Dokholyan, Shivani. S. Godbole, 2023, bioRxiv.

Computational Protein Design Through Grafting and Stabilization.

Nikolay V Dokholyan, David D Mowrey, Cheng Zhu, 2017, Methods in molecular biology.

Light-cleavable Rapamycin Dimer as an Optical Trigger for Protein Dimerization † Chemcomm Communication

N. Dokholyan, D. Shirvanyants, A. Deiters, 2022 .

Elucidation of the Molecular Basis and Cellular Functions of Vinculin-Actin Directional Catch Bonding

N. Dokholyan, S. Campbell, V. Chirasani, 2023, Research square.

Allosteric inactivation of an engineered optogenetic GTPase

Andrew L. Lee, N. Dokholyan, Abha Jain, 2022, bioRxiv.

Bioinformatics Applications Note Ifoldrna: Three-dimensional Rna Structure Prediction and Folding

F. Ding, N. Dokholyan, Shantanu Sharma, 2022 .

Distinct Binding Modes of Vinculin Isoforms Underlie Their Functional Differences.

N. Dokholyan, A. Krokhotin, J. Griffith, 2019, Structure.

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 .

Differentiable rotamer sampling with molecular force fields

Congzhou M. Sha, N. Dokholyan, Jian Wang, 2023, arXiv.org.

Invited: Drug Discovery Approaches using Quantum Machine Learning

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

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

Charles L. Brooks, Adrian W. R. Serohijos, John Moult, 2009, Nature Reviews Drug Discovery.

Computational design of a PAK1 binding protein.

Shuangye Yin, B. Kuhlman, N. Dokholyan, 2010, Journal of molecular biology.

Discrete Molecular Dynamics Can Predict Helical Prestructured Motifs in Disordered Proteins

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

Structural Mechanism of S-Adenosyl Methionine Binding to Catechol O-Methyltransferase

N. Dokholyan, L. Diatchenko, Douglas Tsao, 2011, PloS one.

Rationally designed carbohydrate-occluded epitopes elicit HIV-1 Env-specific antibodies

E. L. Potter, Shamit S. Prabhu, H. Ke, 2019, Nature Communications.

Molecular modeling tools and approaches for CFTR and cystic fibrosis.

Adrian W. R. Serohijos, N. Dokholyan, P. Thibodeau, 2011, Methods in molecular biology.

Using percolation theory to predict oil field performance

H. Stanley, S. Havlin, S. Buldyrev, 2002 .

Identification of posttranscriptional modifications in nucleic acid sequences using propose-designed molecular beacons

James Ze Wang, Jennifer C. Jones, N. Dokholyan, 2023 .

Highly Covarying Residues Have a Functional Role in Antibody Constant Domains

N. Dokholyan, E. Proctor, P. Kota, 2022 .

The evolution dynamics of model proteins.

E. Shakhnovich, R. Broglia, G. Tiana, 2004, The Journal of chemical physics.

Quantifying network behavior in the rat prefrontal cortex: a reproducibility crisis

Congzhou M. Sha, R. Mailman, N. Dokholyan, 2023, bioRxiv.

Activation of Disulfide Redox Switch in REDD1 Promotes Oxidative Stress Under Hyperglycemic Conditions

Congzhou M. Sha, N. Dokholyan, S. Kimball, 2022, Diabetes.

NeuralDock: Rapid and Conformation-Agnostic Docking of Small Molecules

Congzhou M. Sha, N. Dokholyan, Jian Wang, 2021, bioRxiv.

Parallel folding pathways in the SH3 domain protein.

E. Shakhnovich, S. Buldyrev, J. Borreguero, 2007, Journal of molecular biology.

Parallel Folding Pathways in the SH 3 Domain Protein

H. Stanley, S. Buldyrev, J. Borreguero, 2007 .

Faculty of 1000 evaluation for Tau reduction prevents neuronal loss and reverses pathological tau deposition and seeding in mice with tauopathy.

N. Dokholyan, E. Proctor, 2018 .

G Protein Mono-ubiquitination by the Rsp5 Ubiquitin Ligase*

B. Kuhlman, H. Dohlman, Michael J. Lee, 2009, Journal of Biological Chemistry.

Robust and Efficient Assessment of Potency (REAP) as a quantitative tool for dose-response curve estimation

N. Dokholyan, V. Chinchilli, Xinyi Liu, 2021, bioRxiv.

RNA–DNA fibers and polygons with controlled immunorecognition activate RNAi, FRET and transcriptional regulation of NF-κB in human cells

N. Dokholyan, M. Dobrovolskaia, K. Afonin, 2018, Nucleic Acids Research.

The complex molecular biology of amyotrophic lateral sclerosis (ALS).

N. Dokholyan, R. Redler, 2012, Progress in molecular biology and translational science.

Computational design of a PAK1 binding protein.

Shuangye Yin, B. Kuhlman, N. Dokholyan, 2010, Journal of Molecular Biology.

Yuel: Compound-Protein Interaction Prediction with High Generalizability

N. Dokholyan, Jian Wang, 2021, bioRxiv.

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

F. Ding, N. Dokholyan, 2013, J. Chem. Inf. Model..

Discrete molecular dynamics distinguishes nativelike binding poses from decoys in difficult targets.

Shuangye Yin, N. Dokholyan, E. Proctor, 2012, Biophysical journal.

RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction.

Christopher A. Lavender, K. Weeks, A. Serganov, 2012, RNA.

Physical Chemistry Chemical Physics Physical Chemistry of Biomolecular Motors and Machines Guest Editor: Anatoly Kolomeisky (rice University) Papers Twist–stretch Coupling and Phase Transition during Dna Supercoiling Opening the Arg-glu Salt Bridge in Myosin: Computational Study the Energetics of Al

Adrian W. R. Serohijos, Del R. Jackson, Mark E. Arsenault, 2009 .

Allosteric regulation of kinase activity in living cells

N. Dokholyan, Shivani. S. Godbole, 2023, bioRxiv.

Adrian W. R. Serohijos, Del R. Jackson, Mark E. Arsenault, 2022 .

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

Katarzyna J Purzycka, K. Weeks, Zhichao Miao, 2017, RNA.

New models of Tetrahymena telomerase RNA from experimentally derived constraints and modeling.

F. Ding, N. Dokholyan, M. Jarstfer, 2012, Journal of the American Chemical Society.

Septins Enable T Cell Contact Guidance via Amoeboid-Mesenchymal Switch

N. Dokholyan, A. Cartagena-Rivera, A. Zhovmer, 2023, bioRxiv.

G Protein Mono-ubiquitination by the Rsp5 Ubiquitin Ligase*

B. Kuhlman, H. Dohlman, Michael J. Lee, 2009, Journal of Biological Chemistry.

Vitamin D Receptor Antagonist MeTC7 Inhibits PD-L1

Richard G. Moore, P. Jurutka, N. Dokholyan, 2023, Cancers.

Reversible and Tunable Photoswitching of Protein Function through Genetic Encoding of Azobenzene Amino Acids in Mammalian Cells

N. Dokholyan, A. Deiters, S. Samanta, 2018, Chembiochem : a European journal of chemical biology.

Correctors of F508 CFTR restore global conformational maturation without thermally stabilizing the mutant protein

N. Dokholyan, P. Kota, A. Aleksandrov, 2014 .

RNA Three-Dimensional Structure Determination Using Experimental Constraints

F. Ding, N. Dokholyan, 2013 .

Rna Three-dimensional Structure Determination Using Experimental Constraints 8.1 Introduction

F. Ding, N. Dokholyan, 2022 .

The coordinated evolution of yeast proteins is constrained by functional modularity.

N. Dokholyan, Yiwen Chen, 2006, Trends in genetics : TIG.

The Coordinated Evolution of Yeast Proteins Is Constrained by Functional Modularity

N. Dokholyan, Yiwen Chen, 2022 .

A physical model reveals the mechanochemistry responsible for dynein's processive motion.

Adrian W. R. Serohijos, T. Elston, N. Dokholyan, 2011, Biophysical journal.

Multiscale approaches for studying energy transduction in dynein.

Adrian W. R. Serohijos, T. Elston, N. Dokholyan, 2009, Physical chemistry chemical physics : PCCP.

Outcome of a workshop on applications of protein models in biomedical research.

Roland L. Dunbrack, David T. Jones, M. Levitt, 2009, Structure.

Molecular basis and cellular functions of vinculin-actin directional catch bonding

N. Dokholyan, B. Hoffman, Juilee N Malavade, 2023, Nature communications.

Faculty Opinions recommendation of Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype.

N. Dokholyan, E. Proctor, 2014 .

Guiding Conventional Protein-Ligand Docking Software with Convolutional Neural Networks

Mehrdad Mahdavi, Anup Sarma, Huaipan Jiang, 2020, J. Chem. Inf. Model..

Structural bioinformatics Rigid substructure search

N. Dokholyan, D. Shirvanyants, A. Alexandrova, 2011 .

Systematic review and meta-analysis of dysregulated microRNAs derived from liquid biopsies as biomarkers for amyotrophic lateral sclerosis

Congzhou M. Sha, N. Dokholyan, Hemerson Casado Gama, 2024, Non-coding RNA research.

Septin-Mediated Mechanobiological Reprogramming of T Cell Transmigration and 3D Motility

N. Dokholyan, A. Cartagena-Rivera, A. Zhovmer, 2022 .

Structural and Dynamic Insights Into α-Synuclein Dimer Conformations

N. Dokholyan, Nir Kalisman, E. Lerner, 2019, bioRxiv.

Ab initio folding of proteins with all-atom discrete molecular dynamics.

F. Ding, N. Dokholyan, Huifen Nie, 2008, Structure.

Locking and Unlocking Thrombin Function Using Immunoquiescent Nucleic Acid Nanoparticles with Regulated Retention In Vivo.

N. Dokholyan, D. Dréau, M. Dobrovolskaia, 2022, Nano letters.

Antinociceptive Effects of Cannabichromene (CBC) in Mice: Insights from von Frey, Tail-Flick, Formalin, and Acetone Tests

N. Dokholyan, W. Raup-Konsavage, N. Graziane, 2023, Biomedicines.

μ-Opioid receptor 6-transmembrane isoform: A potential therapeutic target for new effective opioids

W. Maixner, N. Dokholyan, M. Gold, 2015, Progress in Neuro-Psychopharmacology and Biological Psychiatry.

REAP-2: An interactive quantitative tool for robust and efficient dose-response curve estimation

N. Dokholyan, Shouhao Zhou, Xinying Fang, 2023, Journal of Clinical and Translational Science.

Dynamics intrinsic to cystic fibrosis transmembrane conductance regulator function and stability.

N. Dokholyan, J. Forman-Kay, P. Kota, 2013, Cold Spring Harbor Perspectives in Medicine.

Highly covarying residues have a functional role in antibody constant domains

N. Dokholyan, E. Proctor, P. Kota, 2013, Proteins.

Rational peptide design for targeting cancer cell invasion

N. Dokholyan, S. Balalaie, Sorour Ramezanpour, 2023, Proteins.

Computational modeling of biological systems : from molecules to pathways

N. Dokholyan, 2012 .

Uncertainty in oil production predicted by percolation theory

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

Unveiling the double-edged sword: SOD1 trimers possess tissue-selective toxicity and bind septin-7 in motor neuron-like cells

Congzhou M. Sha, N. Dokholyan, Brianna Hnath, 2024, bioRxiv.