Author details

Full Name

Eugene I Shakhnovich

Affiliation

Harvard University

ORCID

Career Start Year

1980

Papers

294

H Index

Expertise

CM4AI Collaborator

Andrej Sali (CM4AI)

PMID	Paper Title	Journal Title	Published Year
37577536	Biophysical principles predict fitness of SARS-CoV-2 variants.	bioRxiv	2024
36776823	Systematic conformation-to-phenotype mapping via limited deep-sequencing of proteins.	ArXiv	2023
37873097	Separation of sticker-spacer energetics governs the coalescence of metastable biomolecular condensates.	bioRxiv	2023
37671878	Mapping the Space of Photoswitchable Ligands and Photodruggable Proteins with Computational Modeling.	J Chem Inf Model	2023
37422697	Co-translational formation of disulfides guides folding of the SARS-CoV-2 receptor binding domain.	Biophys J	2023
37155880	Phosphorylation sites are evolutionary checkpoints against liquid-solid transition in protein condensates.	Proc Natl Acad Sci U S A	2023
37267908	Systematic conformation-to-phenotype mapping via limited deep sequencing of proteins.	Mol Cell	2023
37296102	Empowering drug off-target discovery with metabolic and structural analysis.	Nat Commun	2023
37094144	Allosteric communication between ligand binding domains modulates substrate inhibition in adenylate kinase.	Proc Natl Acad Sci U S A	2023
37066177	Epistasis meets pleiotropy in shaping biophysical protein subspaces associated with antimicrobial resistance.	bioRxiv	2023
36844486	Thermal Half-Lives of Azobenzene Derivatives: Virtual Screening Based on Intersystem Crossing Using a Machine Learning Potential.	ACS Cent Sci	2023
36350032	Different states and the associated fates of biomolecular condensates.	Essays Biochem	2022
35705543	Excited state non-adiabatic dynamics of large photoswitchable molecules using a chemically transferable machine learning potential.	Nat Commun	2022
35702028	The physics of liquid-to-solid transitions in multi-domain protein condensates.	Biophys J	2022
35723573	A native chemical chaperone in the human eye lens.	Elife	2022
36380756	Cotranslational formation of disulfides guides folding of the SARS COV-2 receptor binding domain.	bioRxiv	2022
34279221	Development of antibacterial compounds that constrain evolutionary pathways to resistance.	Elife	2021
33932438	Avoidance of protein unfolding constrains protein stability in long-term evolution.	Biophys J	2021
34571014	Switching an active site helix in dihydrofolate reductase reveals limits to subdomain modularity.	Biophys J	2021
33969989	Effect of RNA on Morphology and Dynamics of Membraneless Organelles.	J Phys Chem B	2021
34180142	Metabolic response to point mutations reveals principles of modulation of in vivo enzyme activity and phenotype.	Mol Syst Biol	2021
34168840	Accelerating high-throughput virtual screening through molecular pool-based active learning.	Chem Sci	2021
32484438	Dynamic metastable long-living droplets formed by sticker-spacer proteins.	Elife	2020
31911473	Cotranslational folding allows misfolding-prone proteins to circumvent deep kinetic traps.	Proc Natl Acad Sci U S A	2020
31733243	Semi-rational design and molecular dynamics simulations study of the thermostability enhancement of cellobiose 2-epimerases.	Int J Biol Macromol	2020
33196646	Validation of DBFOLD: An efficient algorithm for computing folding pathways of complex proteins.	PLoS Comput Biol	2020
32857962	Effect of Protein Structure on Evolution of Cotranslational Folding.	Biophys J	2020
32416078	Effects of Single Mutations on Protein Stability Are Gaussian Distributed.	Biophys J	2020
30934244	Mutation rate variability as a driving force in adaptive evolution.	Phys Rev E	2019
31855179	Common activation mechanism of class A GPCRs.	Elife	2019
31416179	The Early Phase of Î²2m Aggregation: An Integrative Computational Study Framed on the D76N Mutant and the Î¿N6 Variant.	Biomolecules	2019
31573512	Adaptation to mutational inactivation of an essential gene converges to an accessible suboptimal fitness peak.	Elife	2019
31401280	Simulation-guided enzyme discovery: A new microbial source of cellobiose 2-epimerase.	Int J Biol Macromol	2019
31097595	Substrate inhibition imposes fitness penalty at high protein stability.	Proc Natl Acad Sci U S A	2019
31095809	Chimeric dihydrofolate reductases display properties of modularity and biophysical diversity.	Protein Sci	2019
29299534	Stability of the Influenza Virus Hemagglutinin Protein Correlates with Evolutionary Dynamics.	mSphere	2018
30242128	Dynamic disulfide exchange in a crystallin protein in the human eye lens promotes cataract-associated aggregation.	J Biol Chem	2018
30097583	Growth tradeoffs produce complex microbial communities on a single limiting resource.	Nat Commun	2018
29883608	Accessibility of the Shine-Dalgarno Sequence Dictates N-Terminal Codon Bias in E.Â coli.	Mol Cell	2018
30091592	Accurate Protein-Folding Transition-Path Statistics from a Simple Free-Energy Landscape.	J Phys Chem B	2018
30010795	ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes.	Bioinformatics	2018
29955873	Evolution on the Biophysical Fitness Landscape of an RNA Virus.	Mol Biol Evol	2018
29445020	Trade-offs between microbial growth phases lead to frequency-dependent and non-transitive selection.	Proc Biol Sci	2018
29630824	Differential Enzyme Flexibility Probed Using Solid-State Nanopores.	ACS Nano	2018
29688000	Correction to Rational Design of Novel Allosteric Dihydrofolate Reductase Inhibitors Showing Antibacterial Effects on Drug-Resistant Escherichia coli Escape Variants.	ACS Chem Biol	2018
29741573	ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes.	Bioinformatics	2018
27810574	Bridging the physical scales in evolutionary biology: from protein sequence space to fitness of organisms and populations.	Curr Opin Struct Biol	2017
28282198	Graph's Topology and Free Energy of a Spin Model on the Graph.	Phys Rev Lett	2017
28191941	A Hybrid Knowledge-Based and Empirical Scoring Function for Protein-Ligand Interaction: SMoG2016.	J Chem Inf Model	2017
28402878	The Role of Evolutionary Selection in the Dynamics of Protein Structure Evolution.	Biophys J	2017

1 - 50 of 294

Ignacia Echeverria

University of California san francisco

Career Start Year 2010

Number of shared co-authors 1

Massimiliano Bonomi

Institut Pasteur, Universite Paris Cite, CNRS UMR 8

Career Start Year 2007

Number of shared co-authors 3

Yanxin Liu

University of California san francisco

Career Start Year 2007

Number of shared co-authors 1

James S Fraser

University of California san francisco

Career Start Year 2006

Number of shared co-authors 4

Abhishek K Jha

Elucidata Corporation

Career Start Year 2005

Number of shared co-authors 1

Timothy R Lezon

University of Pittsburgh

Career Start Year 2004

Number of shared co-authors 2

Sanbo Qin

University of Illinois at Chicago

Career Start Year 2004

Number of shared co-authors 1

Riccardo Pellarin

CNRS UMR 5086 and Universite Claude Bernard Lyon 1

Career Start Year 2003

Number of shared co-authors 2

Peter L Freddolino

University of Michigan ann arbor

Career Start Year 2002

Number of shared co-authors 1

Henry van den Bedem

University of California San Francisco

Career Start Year 2002

Number of shared co-authors 2

Matteo Dal Peraro

Institute of Bioengineering

Career Start Year 2001

Number of shared co-authors 1

Michael Feig

Michigan State University

Career Start Year 1998

Number of shared co-authors 4

Yu Xia

College of Information Engineering, Zhejiang University of Technology

Career Start Year 1996

Number of shared co-authors 2

Jeffery G Saven

University of Pennsylvania

Career Start Year 1996

Number of shared co-authors 1

Gerhard Hummer

Max Planck Institute of Biophysics

Career Start Year 1994

Number of shared co-authors 1

Giorgio Colombo

Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico

Career Start Year 1993

Number of shared co-authors 0

Tanja Kortemme

University of California san francisco

Career Start Year 1993

Number of shared co-authors 5

Huan-Xiang Zhou

University of Illinois Chicago

Career Start Year 1993

Number of shared co-authors 3

Tobin R Sosnick

Institute for Biophysical Dynamics, The University of Chicago

Career Start Year 1990

Number of shared co-authors 3

Carlos J Camacho

University of Pittsburgh

Career Start Year 1990

Number of shared co-authors 1

Rebecca C Wade

Center for Molecular Biology (ZMBH), Heidelberg University

Career Start Year 1989

Number of shared co-authors 2

David Baker

University of Washington

Career Start Year 1988

Number of shared co-authors 7

Haruki Nakamura

Institute for Protein Research, Osaka University

Career Start Year 1980

Number of shared co-authors 1

Ruth Nussinov

Sackler School of Medicine, Tel Aviv University

Career Start Year 1980

Number of shared co-authors 3

David A Case

Rutgers University

Career Start Year 1977

Number of shared co-authors 5

Shoshana J Wodak

VIB-VUB Center for Structural Biology

Career Start Year 1975

Number of shared co-authors 2

Barry Honig

Columbia University Irving Medical Center

Career Start Year 1971

Number of shared co-authors 3

Michael Levitt

Stanford University

Career Start Year 1969

Number of shared co-authors 3

Ron Elber

Institute for Computational Engineering and Science, University of Texas at Austin

Career Start Year 1969

Number of shared co-authors 2

David Eisenberg

university of california los angeles

Career Start Year 1963

Number of shared co-authors 1

row(s) 1 - 30 of 30

Nikolay V Dokholyan

Pennsylvania State University College of Medicine

Co-authored papers 17

Leonid A Mirny

Co-authored papers 13

Bharat V Adkar

Harvard University

Co-authored papers 7

Lewyn Li

Dana-Farber Cancer Institute, Harvard Medical School

Co-authored papers 6

Martin Karplus

Harvard University

Co-authored papers 4

Bogdan Budnik

Co-authored papers 4

Orr Ashenberg

Co-authored papers 3

Charles DeLisi

Co-authored papers 3

Andrew Pekosz

Co-authored papers 2

Hanspeter Pfister

Co-authored papers 2

Michael Morrissey

Co-authored papers 2

Paul Matsudaira

Center for BioImaging Sciences (CBIS), National University of Singapore

Co-authored papers 2

Suwen Zhao

ShanghaiTech University, China iHuman Institute

Co-authored papers 2

Stephen W Michnick

Co-authored papers 2

Kasper Dinkla

Co-authored papers 2

Sergei Maslov

University of Illinois Urbana-Champaign

Co-authored papers 2

David A Weitz

Co-authored papers 2

Hendrik Strobelt

Co-authored papers 2

Andrej Sali (CM4AI)

University of California San Francisco

Co-authored papers 2

Stuart L Schreiber

Broad Institute

Co-authored papers 1

Gabriel F Berriz

Harvard Medical School

Co-authored papers 1

Dietlind L Gerloff

Foundation for Applied Molecular Evolution (FfAME)

Co-authored papers 1

Bernhard O Palsson

University of California San Diego

Co-authored papers 1

Tomasz Zemojtel

Berlin Institute of Health (BIH)

Co-authored papers 1

Paul D Thomas

University of Southern California

Co-authored papers 1

Michele Vendruscolo

University of Cambridge

Co-authored papers 1

Ivet Bahar

Laufer Center for Physical and Quantitative Biology, Stony Brook University

Co-authored papers 1

Madan Mohan Babu

St. Jude Children's Research Hospital

Co-authored papers 1

Boris Reva

Icahn School of Medicine at Mount Sinai

Co-authored papers 1

Orly Dym

Weizmann Institute of Science

Co-authored papers 1

1 - 30

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