Electrostatics, structure prediction, and the energy landscapes for protein folding and binding

Modulation of folding energy landscape by charge–charge interactions: Linking experiments with computational modeling

(2015) Franco O. Tzul et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Frustration in biomolecules

(2014) Diego U. Ferreiro et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Weak Frustration Regulates Sliding and Binding Kinetics on Rugged Protein–DNA Landscapes

(2013) Amir Marcovitz et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protein recognition and selection through conformational and mutually induced fit

(2013) Q. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues

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

Electrostatically Accelerated Encounter and Folding for Facile Recognition of Intrinsically Disordered Proteins

(2013) Debabani Ganguly et al.   PLoS Computational Biology

Electrostatically Accelerated Coupled Binding and Folding of Intrinsically Disordered Proteins

(2012) Debabani Ganguly et al.   JOURNAL OF MOLECULAR BIOLOGY

AWSEM-MD: Protein Structure Prediction Using Coarse-Grained Physical Potentials and Bioinformatically Based Local Structure Biasing

(2012) Aram Davtyan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protein frustratometer: a tool to localize energetic frustration in protein molecules

(2012) M. Jenik et al.   NUCLEIC ACIDS RESEARCH

Folding without charges

(2012) M. Kurnik et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein folding kinetics and thermodynamics from atomistic simulation

(2012) S. Piana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predictive energy landscapes for protein-protein association

(2012) W. Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Correlated Electrostatic Mutations Provide a Reservoir of Stability in HIV Protease

(2012) Omar Haq et al.   PLoS Computational Biology

Frustration in protein-DNA binding influences conformational switching and target search kinetics

(2011) A. Marcovitz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Kinetic consequences of native state optimization of surface-exposed electrostatic interactions in the Fyn SH3 domain

(2011) Arash Zarrine-Afsar et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Automated Prediction of Protein Association Rate Constants

(2011) Sanbo Qin et al.   STRUCTURE

The Effect of Macromolecular Crowding, Ionic Strength and Calcium Binding on Calmodulin Dynamics

(2011) Qian Wang et al.   PLoS Computational Biology

Tackling Force-Field Bias in Protein Folding Simulations: Folding of Villin HP35 and Pin WW Domains in Explicit Water

(2010) Jeetain Mittal et al.   BIOPHYSICAL JOURNAL

The shape of the DNA minor groove directs binding by the DNA-bending protein Fis

(2010) S. Stella et al.   GENES & DEVELOPMENT

Net charge per residue modulates conformational ensembles of intrinsically disordered proteins

(2010) A. H. Mao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Topology-based modeling of intrinsically disordered proteins: Balancing intrinsic folding and intermolecular interactions

(2010) Debabani Ganguly et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Fundamental Aspects of Protein−Protein Association Kinetics

(2009) G. Schreiber et al.   CHEMICAL REVIEWS

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

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

Electrostatic effects on funneled landscapes and structural diversity in denatured protein ensembles

(2009) Patrick Weinkam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein Sliding along DNA: Dynamics and Structural Characterization

(2008) Ohad Givaty et al.   JOURNAL OF MOLECULAR BIOLOGY

Binding-Induced Folding of a Natively Unstructured Transcription Factor

(2008) Adrian Gustavo Turjanski et al.   PLoS Computational Biology