Author details

Full Name

Stephen C Harvey

Affiliation

University of Pennsylvania

ORCID

Career Start Year

1972

Papers

149

H Index

Expertise

CM4AI Collaborator

Andrej Sali (CM4AI)

PMID	Paper Title	Journal Title	Published Year
33119757	Function of a viral genome packaging motor from bacteriophage T4 is insensitive to DNA sequence.	Nucleic Acids Res	2020
31103227	DNA Conformational Changes Play a Force-Generating Role during Bacteriophage Genome Packaging.	Biophys J	2019
30420606	The entropic force generated by intrinsically disordered segments tunes protein function.	Nature	2018
27214211	DNA Scrunching in the Packaging of Viral Genomes.	J Phys Chem B	2016
27135262	Transitions of Double-Stranded DNA Between the A- and B-Forms.	J Phys Chem B	2016
25486612	The scrunchworm hypothesis: transitions between A-DNA and B-DNA provide the driving force for genome packaging in double-stranded DNA bacteriophages.	J Struct Biol	2015
26245571	Productivity: Social impacts of science metrics.	Nature	2015
26621738	History of the ribosome and the origin of translation.	Proc Natl Acad Sci U S A	2015
25752599	Visualizing the global secondary structure of a viral RNA genome with cryo-electron microscopy.	RNA	2015
24461024	Comment on the letter by A. Ben-Shaul: "entropy, energy, and bending of DNA in viral capsids".	Biophys J	2014
25340471	RiboVision suite for visualization and analysis of ribosomes.	Faraday Discuss	2014
24982194	Evolution of the ribosome at atomic resolution.	Proc Natl Acad Sci U S A	2014
24505437	Secondary structures of rRNAs from all three domains of life.	PLoS One	2014
23349871	In vitro secondary structure of the genomic RNA of satellite tobacco mosaic virus.	PLoS One	2013
24086355	Modeling the conformational changes underlying channel opening in CFTR.	PLoS One	2013
23860866	The icosahedral RNA virus as a grotto: organizing the genome into stalagmites and stalactites.	J Biol Phys	2013
23695635	RNA with iron(II) as a cofactor catalyses electron transfer.	Nat Chem	2013
23771137	Secondary structure and domain architecture of the 23S and 5S rRNAs.	Nucleic Acids Res	2013
23399864	Effects of pulling forces, osmotic pressure, condensing agents and viscosity on the thermodynamics and kinetics of DNA ejection from bacteriophages to bacterial cells: a computational study.	J Phys Condens Matter	2013
23269804	Biophysical and ultrastructural characterization of adeno-associated virus capsid uncoating and genome release.	J Virol	2013
23355613	Molecular paleontology: a biochemical model of the ancestral ribosome.	Nucleic Acids Res	2013
22334759	Domain III of the T. thermophilus 23S rRNA folds independently to a near-native state.	RNA	2012
22701543	RNA folding and catalysis mediated by iron (II).	PLoS One	2012
22750417	A model for the structure of satellite tobacco mosaic virus.	J Struct Biol	2012
22747589	GTfold: enabling parallel RNA secondary structure prediction on multi-core desktops.	BMC Res Notes	2012
22712611	RNA-magnesium-protein interactions in large ribosomal subunit.	J Phys Chem B	2012
22879944	Relating the disease mutation spectrum to the evolution of the cystic fibrosis transmembrane conductance regulator (CFTR).	PLoS One	2012
22905742	The entropic cost of polymer confinement.	J Phys Chem B	2012
21187237	Computational approaches to modeling viral structure and assembly.	Methods Enzymol	2011
21379327	Molecular dynamics simulations of forced unbending of integrin Î±(v)Î²â¿¿.	PLoS Comput Biol	2011
21074621	Role of DNA-DNA interactions on the structure and thermodynamics of bacteriophages Lambda and P4.	J Struct Biol	2011
21174452	Computational screening and design of DNA-linked molecular nanowires.	Nano Lett	2011
21173199	Bidentate RNA-magnesium clamps: on the origin of the special role of magnesium in RNA folding.	RNA	2011
19226622	Structural and electrostatic characterization of pariacoto virus: implications for viral assembly.	Biopolymers	2009
20145801	Viral assembly: a molecular modeling perspective.	Phys Chem Chem Phys	2009
20004163	Comprehensive molecular structure of the eukaryotic ribosome.	Structure	2009
19792158	Characterization of DNA conformation inside bacterial viruses.	Phys Rev E Stat Nonlin Soft Matter Phys	2009
19132923	Integration host factor (IHF) dictates the structure of polyamine-DNA condensates: implications for the role of IHF in the compaction of bacterial chromatin.	Biochemistry	2009
18192353	The role of DNA twist in the packaging of viral genomes.	Biophys J	2008
18572416	YUP.SCX: coaxing atomic models into medium resolution electron density maps.	J Struct Biol	2008
18487310	Packaging double-helical DNA into viral capsids: structures, forces, and energetics.	Biophys J	2008
17223529	Structural and thermodynamic principles of viral packaging.	Structure	2007
17919923	The conformation of double-stranded DNA inside bacteriophages depends on capsid size and shape.	J Struct Biol	2007
17573426	DNA organization and thermodynamics during viral packing.	Biophys J	2007
17637341	Packaging of DNA by bacteriophage epsilon15: structure, forces, and thermodynamics.	Structure	2007
16581834	Novel changes in discoidal high density lipoprotein morphology: a molecular dynamics study.	Biophys J	2006
22844233	YUP: A Molecular Simulation Program for Coarse-Grained and Multi-Scaled Models.	J Chem Theory Comput	2006
17090004	DNA-directed assembly of polyanilines: modified cytosine nucleotides transfer sequence programmability to a conjoined polymer.	J Am Chem Soc	2006
16484377	The RNA Ontology Consortium: an open invitation to the RNA community.	RNA	2006
16510155	A structural model for the large subunit of the mammalian mitochondrial ribosome.	J Mol Biol	2006

1 - 50 of 149

Ignacia Echeverria

University of California san francisco

Career Start Year 2010

Number of shared co-authors 2

Arkadiusz W Kulczyk

Institute for Quantitative Biomedicine, Rutgers University

Career Start Year 2004

Number of shared co-authors 4

Ivaylo Ivanov

Georgia State University, GA 30302 USA Center for Diagnostics and Therapeutics

Career Start Year 2002

Number of shared co-authors 0

Peter L Freddolino

University of Michigan ann arbor

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 5

Lewyn Li

Dana-Farber Cancer Institute, Harvard Medical School

Career Start Year 2000

Number of shared co-authors 0

Michael Feig

Michigan State University

Career Start Year 1998

Number of shared co-authors 1

Nikolay V Dokholyan

Pennsylvania State University College of Medicine

Career Start Year 1998

Number of shared co-authors 7

Cameron Mura

University of Virginia

Career Start Year 1998

Number of shared co-authors 0

Aaron R Dinner

James Franck Institute, Institute for Biophysical Dynamics, University of Chicago

Career Start Year 1996

Number of shared co-authors 1

Liping Wang

The University of Texas Health Science Center at San Antonio

Career Start Year 1995

Number of shared co-authors 0

Gerhard Hummer

Max Planck Institute of Biophysics

Career Start Year 1994

Number of shared co-authors 5

Huan-Xiang Zhou

University of Illinois Chicago

Career Start Year 1993

Number of shared co-authors 2

Koen Visscher

Inscopix Inc.

Career Start Year 1991

Number of shared co-authors 1

Tobin R Sosnick

Institute for Biophysical Dynamics, The University of Chicago

Career Start Year 1990

Number of shared co-authors 6

John F Hunt

Columbia University

Career Start Year 1986

Number of shared co-authors 8

Michael Nilges

Institut Pasteur

Career Start Year 1986

Number of shared co-authors 5

Ariel Fern??ndez

University of Florida

Career Start Year 1984

Number of shared co-authors 0

Ruth Nussinov

Sackler School of Medicine, Tel Aviv University

Career Start Year 1980

Number of shared co-authors 5

Eugene I Shakhnovich

Harvard University

Career Start Year 1980

Number of shared co-authors 1

Carlos Bustamante

University of California berkeley

Career Start Year 1979

Number of shared co-authors 0

Edward H Egelman

University of Virginia

Career Start Year 1979

Number of shared co-authors 6

David A Case

Rutgers University

Career Start Year 1977

Number of shared co-authors 5

Charles L Brooks

University of Michigan ann arbor

Career Start Year 1974

Number of shared co-authors 3

Alain Laederach

University of North Carolina at Chapel Hill

Career Start Year 1972

Number of shared co-authors 3

Dinshaw J Patel

Memorial Sloan-Kettering Cancer Center

Career Start Year 1969

Number of shared co-authors 3

Michael Levitt

Stanford University

Career Start Year 1969

Number of shared co-authors 7

Ron Elber

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

Career Start Year 1969

Number of shared co-authors 1

Sung-Hou Kim

University of California berkeley

Career Start Year 1967

Number of shared co-authors 4

Martin Karplus

Harvard University

Career Start Year 1959

Number of shared co-authors 3

row(s) 1 - 30 of 30

Scott M Stagg

Florida State University

Co-authored papers 8

James Andrew McCammon

Co-authored papers 8

Margaret S VanLoock

University of Virginia Health Sciences Center

Co-authored papers 7

Arun Malhotra

University of Miami Miller School of Medicine

Co-authored papers 5

Batsal Devkota

Children's Hospital of Philadelphia

Co-authored papers 5

Joachim Frank

Columbia University

Co-authored papers 5

Rajendra K Agrawal

School of Public Health, University at Albany

Co-authored papers 5

Robin R Gutell

The University of Texas at Austin

Co-authored papers 3

Mikel Valle

Center for Cooperative Research in Biosciences (CIC bioGUNE)

Co-authored papers 3

Andrej Sali (CM4AI)

University of California San Francisco

Co-authored papers 2

Russ B Altman

Stanford University

Co-authored papers 2

Jayati Sengupta

Institute of Child Health

Co-authored papers 2

Helen M Berman

The State University of New Jersey

Co-authored papers 2

James C Gumbart

Georgia Institute of Technology

Co-authored papers 2

Neocles B Leontis

Bowling Green State University

Co-authored papers 2

Narayanan Eswar

University of California at San Francisco

Co-authored papers 2

Nael A McCarty

Emory University

Co-authored papers 2

Jamie J Cannone

The University of Texas at Austin

Co-authored papers 2

Patrick Gendron

University of Montreal

Co-authored papers 1

Andrei A Korostelev

RNA Therapeutics Institute, University of Massachusetts Chan Medical School

Co-authored papers 1

Patrick Van Roey

Center for Medical Sciences

Co-authored papers 1

Steven E Brenner

University of California berkeley

Co-authored papers 1

Suzanna E Lewis

Lawrence Berkeley National Laboratory

Co-authored papers 1

Jessica K Peters

Department of Pharmaceutical Chemistry, University of California san francisco

Co-authored papers 1

Barry Honig

Columbia University Irving Medical Center

Co-authored papers 1

William F Marzluff

University of North Carolina at Chapel Hill

Co-authored papers 1

Derek J Taylor

Case Western Reserve University

Co-authored papers 1

Maya Topf

Leibniz-Institut fur Virologie (LIV)

Co-authored papers 1

Neha Varghese

Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory

Co-authored papers 1

William M Gelbart

University of California Los Angeles

Co-authored papers 1

1 - 30

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