Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

(2015) Robert T. McGibbon et al.   BIOPHYSICAL JOURNAL

Theoretical perspectives on nonnative interactions and intrinsic disorder in protein folding and binding

(2015) Tao Chen et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States

(2015) Stefano Piana et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Comprehensive analysis of sequences of a protein switch

(2015) Szu-Hua Chen et al.   PROTEIN SCIENCE

Native Contact Density and Nonnative Hydrophobic Effects in the Folding of Bacterial Immunity Proteins

(2015) Tao Chen et al.   PLoS Computational Biology

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

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

Smooth Functional Transition along a Mutational Pathway with an Abrupt Protein Fold Switch

(2014) Christian Holzgräfe et al.   BIOPHYSICAL JOURNAL

Complex Pathways in Folding of Protein G Explored by Simulation and Experiment

(2014) Lisa J. Lapidus et al.   BIOPHYSICAL JOURNAL

Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations

(2014) Stefano Piana et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Modeling Non-Native Interactions in Designed Proteins

(2014) Shilpa Yadahalli et al.   ISRAEL JOURNAL OF CHEMISTRY

Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model

(2014) Michael Knott et al.   JOURNAL OF CHEMICAL PHYSICS

Pressure-Dependent Properties of Elementary Hydrophobic Interactions: Ramifications for Activation Properties of Protein Folding

(2014) Cristiano L. Dias et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Biophysics of protein evolution and evolutionary protein biophysics

(2014) T. Sikosek et al.   Journal of the Royal Society Interface

The energy landscape of a protein switch

(2014) Szu-Hua Chen et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Effects of desolvation barriers and sidechains on local–nonlocal coupling and chevron behaviors in coarse-grained models of protein folding

(2014) Tao Chen et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Benchmarking all-atom simulations using hydrogen exchange

(2014) John J. Skinner 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

A Simulated Intermediate State for Folding and Aggregation Provides Insights into ΔN6 β2-Microglobulin Amyloidogenic Behavior

(2014) Sílvia G. Estácio et al.   PLoS Computational Biology

Relative Free Enthalpies for Point Mutations in Two Proteins with Highly Similar Sequences but Different Folds

(2013) Niels Hansen et al.   BIOCHEMISTRY

Evolutionary biochemistry: revealing the historical and physical causes of protein properties

(2013) Michael J. Harms et al.   NATURE REVIEWS GENETICS

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era

(2013) H. Kamisetty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Atomic-level description of ubiquitin folding

(2013) S. Piana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiscaled exploration of coupled folding and binding of an intrinsically disordered molecular recognition element in measles virus nucleoprotein

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

Folding of Top7 in unbiased all-atom Monte Carlo simulations

(2013) Sandipan Mohanty et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Computing the Relative Stabilities and the Per-Residue Components in Protein Conformational Changes

(2013) Arijit Roy et al.   STRUCTURE

From A to B: A ride in the free energy surfaces of protein G domains suggests how new folds arise

(2012) Ludovico Sutto et al.   JOURNAL OF CHEMICAL PHYSICS

Modeling Structural Flexibility of Proteins with Go-Models

(2012) Ping Jiang et al.   Journal of Chemical Theory and Computation

Identification of a Conserved Aggregation-Prone Intermediate State in the Folding Pathways of Spc-SH3 Amyloidogenic Variants

(2012) H. Krobath et al.   JOURNAL OF MOLECULAR BIOLOGY

Folding Simulations of the A and B Domains of Protein G

(2012) Maksim Kouza et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Escape from Adaptive Conflict follows from weak functional trade-offs and mutational robustness

(2012) T. Sikosek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Folding pathways of proteins with increasing degree of sequence identities but different structure and function

(2012) R. Giri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Templates are available to model nearly all complexes of structurally characterized proteins

(2012) P. J. Kundrotas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The interface of protein structure, protein biophysics, and molecular evolution

(2012) David A. Liberles et al.   PROTEIN SCIENCE

Mutational Tipping Points for Switching Protein Folds and Functions

(2012) Yanan He et al.   STRUCTURE

Evolutionary Dynamics on Protein Bi-stability Landscapes can Potentially Resolve Adaptive Conflicts

(2012) Tobias Sikosek et al.   PLoS Computational Biology

Aromatic Rings in Chemical and Biological Recognition: Energetics and Structures

(2011) Laura M. Salonen et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

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

Current Computer Modeling Cannot Explain Why Two Highly Similar Sequences Fold into Different Structures

(2011) Jane R. Allison et al.   BIOCHEMISTRY

GB1 Is Not a Two-State Folder: Identification and Characterization of an On-Pathway Intermediate

(2011) Angela Morrone et al.   BIOPHYSICAL JOURNAL

Mutation-induced fold switching among lattice proteins

(2011) Christian Holzgräfe et al.   JOURNAL OF CHEMICAL PHYSICS

A Hybrid All-Atom Structure-Based Model for Protein Folding and Large Scale Conformational Transitions

(2011) Ludovico Sutto et al.   Journal of Chemical Theory and Computation

Solution structure of a minor and transiently formed state of a T4 lysozyme mutant

(2011) Guillaume Bouvignies et al.   NATURE

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

Taming the complexity of protein folding

(2010) Gregory R Bowman et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The Denatured State Dictates the Topology of Two Proteins with Almost Identical Sequence but Different Native Structure and Function

(2010) Angela Morrone et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Competition between native topology and nonnative interactions in simple and complex folding kinetics of natural and designed proteins

(2010) Z. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics

(2009) Ronald Hills et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Lymphotactin: How a protein can adopt two folds

(2009) Carlo Camilloni et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

A minimal sequence code for switching protein structure and function

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

Experimental determination of upper bound for transition path times in protein folding from single-molecule photon-by-photon trajectories

(2009) H. S. Chung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details

(2009) V. Potapov et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Computational exploration of the network of sequence flow between protein structures

(2009) Baoqiang Cao et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

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

Protein Dynamism and Evolvability

(2009) N. Tokuriki et al.   SCIENCE

An effective all-atom potential for proteins

(2009) Anders Irbäck et al.   BMC Biophysics

Thermodynamics of stacking interactions in proteins

(2008) Simone Marsili et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding

(2008) A. Zarrine-Afsar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simulation of Top7-CFr: A transient helix extension guides folding

(2008) S. Mohanty 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

Folding Pathway of the B1 Domain of Protein G Explored by Multiscale Modeling

(2007) Sebastian Kmiecik et al.   BIOPHYSICAL JOURNAL

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

(2002) John Karanicolas et al.   PROTEIN SCIENCE