Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins

Global informatics and physical property selection in protein sequences

(2016) Harold A. Scheraga et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

(2015) Jumin Lee et al.   Journal of Chemical Theory and Computation

New Insights into Protein (Un)Folding Dynamics

(2015) Yoann Cote et al.   Journal of Physical Chemistry Letters

Alternative approach to protein structure prediction based on sequential similarity of physical properties

(2015) Yi He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Homolog detection using global sequence properties suggests an alternate view of structural encoding in protein sequences

(2014) H. A. Scheraga et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modulation of frustration in folding by sequence permutation

(2014) R. P. Nobrega et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative molecular dynamics simulation studies for determining factors contributing to the thermostability of chemotaxis protein “CheY”

(2013) Manish Paul et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Local vs Global Motions in Protein Folding

(2013) Gia G. Maisuradze et al.   Journal of Chemical Theory and Computation

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

(2013) Jing Huang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Native contacts determine protein folding mechanisms in atomistic simulations

(2013) R. B. Best et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

Anomalous diffusion and dynamical correlation between the side chains and the main chain of proteins in their native state

(2012) Y. Cote et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Topological Frustration in βα-Repeat Proteins: Sequence Diversity Modulates the Conserved Folding Mechanisms of α/β/α Sandwich Proteins

(2010) Ronald D. Hills et al.   JOURNAL OF MOLECULAR BIOLOGY

Nonexponential decay of internal rotational correlation functions of native proteins and self-similar structural fluctuations

(2010) Y. Cote et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

LPFC: An internet library of protein family core structures

(2010) Robert Schmidt et al.   PROTEIN SCIENCE

Different Members of a Simple Three-Helix Bundle Protein Family Have Very Different Folding Rate Constants and Fold by Different Mechanisms

(2009) Beth G. Wensley et al.   JOURNAL OF MOLECULAR BIOLOGY

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Subdomain Competition, Cooperativity, and Topological Frustration in the Folding of CheY

(2008) Ronald D. Hills et al.   JOURNAL OF MOLECULAR BIOLOGY

The effect of Asp54 phosphorylation on the energetics and dynamics in the response regulator protein Spo0F studied by molecular dynamics

(2008) Günther H. Peters   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The origins of asymmetry in the folding transition states of protein L and protein G

(2002) John Karanicolas et al.   PROTEIN SCIENCE