Biophysical and structural considerations for protein sequence evolution

Theoretical and Computational Protein Design

(2011) Ilan Samish et al.   Annual Review of Physical Chemistry

The Relationship Between Relative Solvent Accessibility and Evolutionary Rate in Protein Evolution

(2011) Duncan C. Ramsey et al.   GENETICS

Fast Side Chain Replacement in Proteins Using a Coarse-Grained Approach for Evaluating the Effects of Mutation During Evolution

(2011) Johan A. Grahnen et al.   JOURNAL OF MOLECULAR EVOLUTION

Equilibrium Distribution from Distributed Computing (Simulations of Protein Folding)

(2011) Riccardo Scalco et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Maps of protein structure space reveal a fundamental relationship between protein structure and function

(2011) M. Osadchy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Binding constraints on the evolution of enzymes and signalling proteins: the important role of negative pleiotropy

(2011) D. A. Liberles et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

What's in a Likelihood? Simple Models of Protein Evolution and the Contribution of Structurally Viable Reconstructions to the Likelihood

(2011) Clemens Lakner et al.   SYSTEMATIC BIOLOGY

Potentials 'R'Us web-server for protein energy estimations with coarse-grained knowledge-based potentials

(2010) Yaping Feng et al.   BMC BIOINFORMATICS

Live imaging of single nuclear pores reveals unique assembly kinetics and mechanism in interphase

(2010) Elisa Dultz et al.   JOURNAL OF CELL BIOLOGY

Current Status of the AMOEBA Polarizable Force Field

(2010) Jay W. Ponder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Simulation ofab InitioProtein Folding for a Millisecond Folder NTL9(1−39)

(2010) Vincent A. Voelz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Evolution of Structurally Disordered Proteins Promotes Neostructuralization

(2010) J. Siltberg-Liberles   MOLECULAR BIOLOGY AND EVOLUTION

Statistical Potentials for Improved Structurally Constrained Evolutionary Models

(2010) Claudia L. Kleinman et al.   MOLECULAR BIOLOGY AND EVOLUTION

Challenges in protein-folding simulations

(2010) Peter L. Freddolino et al.   Nature Physics

The evolution and evolutionary consequences of marginal thermostability in proteins

(2010) Richard A. Goldstein   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Quantifying the Impact of Dependent Evolution among Sites in Phylogenetic Inference

(2010) Chris A. Nasrallah et al.   SYSTEMATIC BIOLOGY

Multiscale Coarse-Graining of the Protein Energy Landscape

(2010) Ronald D. Hills et al.   PLoS Computational Biology

The SH2 Domains of Inositol Polyphosphate 5-Phosphatases SHIP1 and SHIP2 Have Similar Ligand Specificity but Different Binding Kinetics

(2009) Yanyan Zhang et al.   BIOCHEMISTRY

Comparative Assessment of Scoring Functions on a Diverse Test Set

(2009) Tiejun Cheng et al.   Journal of Chemical Information and Modeling

Solvent accessible surface area approximations for rapid and accurate protein structure prediction

(2009) Elizabeth Durham et al.   JOURNAL OF MOLECULAR MODELING

INDELible: A Flexible Simulator of Biological Sequence Evolution

(2009) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

Structure is three to ten times more conserved than sequence-A study of structural response in protein cores

(2009) Kristoffer Illergård et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Protein Folding Problem

(2008) Ken A. Dill et al.   Annual Review of Biophysics

The structure of protein evolution and the evolution of protein structure

(2008) Richard A Goldstein   CURRENT OPINION IN STRUCTURAL BIOLOGY

Recent advances in implicit solvent-based methods for biomolecular simulations

(2008) Jianhan Chen et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Evaluating and optimizing computational protein design force fields using fixed composition-based negative design

(2008) O. Alvizo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA