Author details

Full Name

Karl F Freed

Affiliation

University of Chicago

ORCID

Career Start Year

1985

Papers

138

H Index

Expertise

CM4AI Collaborator

Andrej Sali (CM4AI)

PMID	Paper Title	Journal Title	Published Year
34936354	Prediction and Validation of a Protein's Free Energy Surface Using Hydrogen Exchange and (Importantly) Its Denaturant Dependence.	J Chem Theory Comput	2022
35213808	Challenges and Advantages of Accounting for Backbone Flexibility in Prediction of Protein-Protein Complexes.	J Chem Theory Comput	2022
31575160	Lattice theory for binding of linear polymers to a solid substrate from polymer melts: I. Influence of chain connectivity on molecular binding and adsorption.	J Chem Phys	2019
31587831	On the Interpretation of Force-Induced Unfolding Studies of Membrane Proteins Using Fast Simulations.	Biophys J	2019
31575163	Lattice theory for binding of linear polymers to a solid substrate from polymer melts. II. Influence of van der Waals interactions and chain semiflexibility on molecular binding and adsorption.	J Chem Phys	2019
30384679	Dielectric virial expansion of polarizable dipolar spheres.	J Chem Phys	2018
30166460	Response to Comment on "Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water".	Science	2018
30068175	Lattice theory of competitive binding: Influence of van der Waals interactions on molecular binding and adsorption to a solid substrate from binary liquid mixtures.	J Chem Phys	2018
30589846	Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics.	PLoS Comput Biol	2018
30589834	Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours.	PLoS Comput Biol	2018
30413241	A Membrane Burial Potential with H-Bonds and Applications to Curved Membranes and Fast Simulations.	Biophys J	2018
28810766	Mixtures of two self- and mutually-associating liquids: Phase behavior, second virial coefficients, and entropy-enthalpy compensation in the free energy of mixing.	J Chem Phys	2017
28176808	Comparative Study of the Collective Dynamics of Proteins and Inorganic Nanoparticles.	Sci Rep	2017
29026044	Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water.	Science	2017
28810793	Image method for electrostatic energy of polarizable dipolar spheres.	J Chem Phys	2017
26896771	A theory of interactions between polarizable dielectric spheres.	J Colloid Interface Sci	2016
35651209	Stringlike Cooperative Motion Explains the Influence of Pressure on Relaxation in a Model Glass-Forming Polymer Melt.	ACS Macro Lett	2016
28010099	Generalized entropy theory of glass-formation in fully flexible polymer melts.	J Chem Phys	2016
27782617	Image method for induced surface charge from many-body system of dielectric spheres.	J Chem Phys	2016
27497583	Erratum: "Ionic strength independence of charge distributions in solvation of biomolecules" [J. Chem. Phys. 141, 22D503 (2014)].	J Chem Phys	2016
27253170	Relation Between Solvent Quality and Phase Behavior of Ternary Mixtures of Polymers and Two Solvents that Exhibit Cononsolvency.	J Phys Chem B	2016
27276966	Self-assembly and glass-formation in a lattice model of telechelic polymer melts: Influence of stiffness of the sticky bonds.	J Chem Phys	2016
27078098	Cooperative folding near the downhill limit determined with amino acid resolution by hydrogen exchange.	Proc Natl Acad Sci U S A	2016
25573581	The meaning of the "universal" WLF parameters of glass-forming polymer liquids.	J Chem Phys	2015
26590552	Phase behavior and second osmotic virial coefficient for competitive polymer solvation in mixed solvent solutions.	J Chem Phys	2015
26450285	Communication: Cosolvency and cononsolvency explained in terms of a Flory-Huggins type theory.	J Chem Phys	2015
26254633	Communication: The simplified generalized entropy theory of glass-formation in polymer melts.	J Chem Phys	2015
26100906	Even with nonnative interactions, the updated folding transition states of the homologs Proteins G & L are extensive and similar.	Proc Natl Acad Sci U S A	2015
26049523	Theory of competitive solvation of polymers by two solvents and entropy-enthalpy compensation in the solvation free energy upon dilution with the second solvent.	J Chem Phys	2015
26178122	Lattice model of linear telechelic polymer melts. II. Influence of chain stiffness on basic thermodynamic properties.	J Chem Phys	2015
26178121	Lattice model of linear telechelic polymer melts. I. Inclusion of chain semiflexibility in the lattice cluster theory.	J Chem Phys	2015
25854259	Lattice cluster theory for dense, thin polymer films.	J Chem Phys	2015
24852557	Concentration fluctuations in miscible polymer blends: influence of temperature and chain rigidity.	J Chem Phys	2014
25494774	Ionic strength independence of charge distributions in solvation of biomolecules.	J Chem Phys	2014
25527959	Advances in the generalized entropy theory of glass-formation in polymer melts.	J Chem Phys	2014
25318708	Communication: Towards first principles theory of relaxation in supercooled liquids formulated in terms of cooperative motion.	J Chem Phys	2014
25313044	Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations.	Proc Natl Acad Sci U S A	2014
25349413	Benchmarking all-atom simulations using hydrogen exchange.	Proc Natl Acad Sci U S A	2014
25053309	Perturbative many-body expansion for electrostatic energy and field for system of polarizable charged spherical ions in a dielectric medium.	J Chem Phys	2014
24985676	Two glass transitions in miscible polymer blends?	J Chem Phys	2014
25084958	Lattice cluster theory for polymer melts with specific interactions.	J Chem Phys	2014
23352932	Molecular origins of cofilin-linked changes in actin filament mechanics.	J Mol Biol	2013
24116582	Phase field method for nonequilibrium dynamics of reversible self-assembly systems.	J Chem Phys	2013
23889448	Simplified protein models: predicting folding pathways and structure using amino acid sequences.	Phys Rev Lett	2013
24010668	A novel implicit solvent model for simulating the molecular dynamics of RNA.	Biophys J	2013
23635166	Solvation of polymers as mutual association. II. Basic thermodynamic properties.	J Chem Phys	2013
23635165	Solvation of polymers as mutual association. I. General theory.	J Chem Phys	2013
23802965	Thermodynamic scaling of dynamics in polymer melts: predictions from the generalized entropy theory.	J Chem Phys	2013
23530611	Theoretical studies of the ground and excited state structures of stilbene.	J Phys Chem A	2013
22095743	Modeling large regions in proteins: applications to loops, termini, and folding.	Protein Sci	2012

1 - 50 of 138

Hythem Sidky

National Center for Advancing Translational Sciences (NCATS)

Career Start Year 2016

Number of shared co-authors 1

Tanmoy Sanyal

University of California san francisco

Career Start Year 2013

Number of shared co-authors 1

David R Slochower

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California

Career Start Year 2010

Number of shared co-authors 0

Adam P Willard

Massachusetts Institute of Technology

Career Start Year 2008

Number of shared co-authors 0

Michel A Cuendet

Precision Oncology Center, Lausanne University Hospital

Career Start Year 2006

Number of shared co-authors 0

Edyta Malolepsza

Broad Institute of MIT and Harvard

Career Start Year 2005

Number of shared co-authors 0

Patrick Varilly

The Broad Institute of MIT and Harvard

Career Start Year 2005

Number of shared co-authors 0

Tiffany R Walsh

Institute for Frontier Materials, Deakin University

Career Start Year 2005

Number of shared co-authors 0

Sanbo Qin

University of Illinois at Chicago

Career Start Year 2004

Number of shared co-authors 2

Peter Prinsen

University of California los angeles

Career Start Year 2003

Number of shared co-authors 0

Riccardo Pellarin

CNRS UMR 5086 and Universite Claude Bernard Lyon 1

Career Start Year 2003

Number of shared co-authors 1

Artem B Mamonov

MGH/Harvard Medical School

Career Start Year 2003

Number of shared co-authors 2

Fabrice Thalmann

Institut Charles Sadron, CNRS UPR22-University of Strasbourg

Career Start Year 2003

Number of shared co-authors 0

David E Shaw

Columbia University

Career Start Year 2000

Number of shared co-authors 1

Itamar Borukhov

Institute of Biotechnology, University of Helsinki

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 2

Aaron R Dinner

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

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

Huan-Xiang Zhou

University of Illinois Chicago

Career Start Year 1993

Number of shared co-authors 2

Carlos M Marques

Institut Charles Sadron, CNRS and University of Strasbourg

Career Start Year 1992

Number of shared co-authors 0

Koen Visscher

Inscopix Inc.

Career Start Year 1991

Number of shared co-authors 2

Francisco Melo

Pontificia Universidad Catolica de Chile

Career Start Year 1989

Number of shared co-authors 2

Michael K Gilson

University of California

Career Start Year 1985

Number of shared co-authors 1

Eugene I Shakhnovich

Harvard University

Career Start Year 1980

Number of shared co-authors 2

David A Case

Rutgers University

Career Start Year 1977

Number of shared co-authors 2

Charles L Brooks

University of Michigan ann arbor

Career Start Year 1974

Number of shared co-authors 1

Ron Elber

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

Career Start Year 1969

Number of shared co-authors 2

Martin Karplus

Harvard University

Career Start Year 1959

Number of shared co-authors 1

row(s) 1 - 30 of 30

Tobin R Sosnick

Institute for Biophysical Dynamics, The University of Chicago

Co-authored papers 39

Abhishek K Jha

Elucidata Corporation

Co-authored papers 11

Min-Yi Shen

National Chung Hsing University

Co-authored papers 7

Andres Colubri

University of Massachusetts Medical School

Co-authored papers 6

Jinbo Xu

Toyota Technological Institute at Chicago

Co-authored papers 4

Jian Peng

University of Illinois

Co-authored papers 3

R Stephen Berry

University of Chicago

Co-authored papers 3

Maxim N Artyomov

Co-authored papers 2

Lee Makowski

Co-authored papers 2

Juan J de Pablo

University of Chicago

Co-authored papers 2

Ariel Fern??ndez

University of Florida

Co-authored papers 1

Andrej Sali (CM4AI)

University of California San Francisco

Co-authored papers 1

Gregory A Voth

Co-authored papers 1

Chaok Seok

Seoul National University

Co-authored papers 1

Cheryl H Arrowsmith

University of Toronto

Co-authored papers 1

Sheng Wang

University of Texas at Arlington

Co-authored papers 1

1 - 16

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