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

Mutational Tipping Points for Switching Protein Folds and Functions

(2012) Yanan He et al.   STRUCTURE

Native-State Interconversion of a Metamorphic Protein Requires Global Unfolding

(2011) Robert C. Tyler et al.   BIOCHEMISTRY

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

Exploring the Thermodynamic Landscape, Kinetics, and Structural Evolution of a Protein Conformational Transition with a Microscopic Double-Well Model

(2011) Zai-Zhi Lai et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Exploring one-state downhill protein folding in single molecules

(2011) J. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How do new proteins arise?

(2010) Erich Bornberg-Bauer et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Proteins that switch folds

(2010) Philip N Bryan 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

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

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

Temperature-dependent structural changes in intrinsically disordered proteins: Formation of α-helices or loss of polyproline II?

(2010) Magnus Kjaergaard et al.   PROTEIN SCIENCE

Improved side-chain torsion potentials for the Amber ff99SB protein force field

(2010) Kresten Lindorff-Larsen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Lymphotactin: How a protein can adopt two folds

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

A designed protein as experimental model of primordial folding

(2009) M. Sadqi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

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

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Origins of barriers and barrierless folding in BBL

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

Comparison of successive transition states for folding reveals alternative early folding pathways of two homologous proteins

(2008) N. Calosci et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interconversion between two unrelated protein folds in the lymphotactin native state

(2008) Robbyn L. Tuinstra 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

BIOCHEMISTRY: Metamorphic Proteins

(2008) A. G. Murzin   SCIENCE

Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms

(2008) Sichun Yang et al.   PLoS Computational Biology