SMOG 2: A Versatile Software Package for Generating Structure-Based Models

Generalized Manning Condensation Model Captures the RNA Ion Atmosphere

(2015) Ryan L. Hayes et al.   PHYSICAL REVIEW LETTERS

Constructing sequence-dependent protein models using coevolutionary information

(2015) Ryan R. Cheng et al.   PROTEIN SCIENCE

Dimeric interactions and complex formation using direct coevolutionary couplings

(2015) Ricardo N. dos Santos et al.   Scientific Reports

Interdomain Contacts Control Native State Switching of RfaH on a Dual-Funneled Landscape

(2015) César A. Ramírez-Sarmiento et al.   PLoS Computational Biology

Capturing Transition Paths and Transition States for Conformational Rearrangements in the Ribosome

(2014) Jeffrey K. Noel et al.   BIOPHYSICAL JOURNAL

From structure to function: the convergence of structure based models and co-evolutionary information

(2014) Biman Jana et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information

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

Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection

(2014) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

eSBMTools 1.0: enhanced native structure-based modeling tools

(2013) Benjamin Lutz et al.   BIOINFORMATICS

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics

(2013) Gongpu Zhao et al.   NATURE

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

Mirror Images as Naturally Competing Conformations in Protein Folding

(2012) Jeffrey K. Noel et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The Shadow Map: A General Contact Definition for Capturing the Dynamics of Biomolecular Folding and Function

(2012) Jeffrey K. Noel et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Biomolecular dynamics: order–disorder transitions and energy landscapes

(2012) Paul C Whitford et al.   REPORTS ON PROGRESS IN PHYSICS

The Origin of Minus-end Directionality and Mechanochemistry of Ncd Motors

(2012) Biman Jana et al.   PLoS Computational Biology

Cooperativity, Local-Nonlocal Coupling, and Nonnative Interactions: Principles of Protein Folding from Coarse-Grained Models

(2011) Hue Sun Chan et al.   Annual Review of Physical Chemistry

Definition and testing of the GROMOS force-field versions 54A7 and 54B7

(2011) Nathan Schmid et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Excited states of ribosome translocation revealed through integrative molecular modeling

(2011) P. C. Whitford et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins

(2011) Wenfei Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The role of atomic level steric effects and attractive forces in protein folding

(2011) Heiko Lammert et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Origin of Nonmonotonic Complex Behavior and the Effects of Nonnative Interactions on the Diffusive Properties of Protein Folding

(2010) Ronaldo J. Oliveira et al.   BIOPHYSICAL JOURNAL

SMOG@ctbp: simplified deployment of structure-based models in GROMACS

(2010) Jeffrey K. Noel et al.   NUCLEIC ACIDS RESEARCH

Slipknotting upon native-like loop formation in a trefoil knot protein

(2010) J. K. Noel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Native Topology of the Designed Protein Top7 is Not Conducive to Cooperative Folding

(2009) Zhuqing Zhang et al.   BIOPHYSICAL JOURNAL

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Nonnative Electrostatic Interactions Can Modulate Protein Folding: Molecular Dynamics with a Grain of Salt

(2009) Ariel Azia et al.   JOURNAL OF MOLECULAR BIOLOGY

Coordinate-dependent diffusion in protein folding

(2009) R. B. Best et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Robustness and generalization of structure-based models for protein folding and function

(2009) Heiko Lammert et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Pulling Direction as a Reaction Coordinate for the Mechanical Unfolding of Single Molecules†

(2008) Robert B. Best et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Quantitative criteria for native energetic heterogeneity influences in the prediction of protein folding kinetics

(2008) S. S. Cho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effect of glycosylation on protein folding: A close look at thermodynamic stabilization

(2008) D. Shental-Bechor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields

(2008) Paul C. Whitford et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Coarse-grained models of protein folding: toy models or predictive tools?

(2007) Cecilia Clementi   CURRENT OPINION IN STRUCTURAL BIOLOGY