The Evolution of Protein Structures and Structural Ensembles Under Functional Constraint

Biophysical and structural considerations for protein sequence evolution

(2011) Johan A Grahnen et al.   BMC EVOLUTIONARY BIOLOGY

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

(2011) Duncan C. Ramsey et al.   GENETICS

Non-adaptive origins of interactome complexity

(2011) Ariel Fernández et al.   NATURE

Markov Models of Amino Acid Substitution to Study Proteins with Intrinsically Disordered Regions

(2011) Adam M. Szalkowski et al.   PLoS One

Experimental illumination of a fitness landscape

(2011) R. T. Hietpas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

A biophysical protein folding model accounts for most mutational fitness effects in viruses

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

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

Protein secondary structure appears to be robust under in silico evolution while protein disorder appears not to be

(2010) Christian Schaefer et al.   BIOINFORMATICS

Analysis of the Bacterial Luciferase Mobile Loop by Replica-Exchange Molecular Dynamics

(2010) Zachary T. Campbell et al.   BIOPHYSICAL JOURNAL

Genome-Wide Influence of Indel Substitutions on Evolution of Bacteria of the PVC Superphylum, Revealed Using a Novel Computational Method

(2010) Olga K. Kamneva et al.   Genome Biology and Evolution

Different Folding Pathways Taken by Highly Homologous Proteins, Goat α-Lactalbumin and Canine Milk Lysozyme

(2010) Takashi Nakamura et al.   JOURNAL OF MOLECULAR BIOLOGY

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

Sequence space and the ongoing expansion of the protein universe

(2010) Inna S. Povolotskaya et al.   NATURE

Mutational effects and the evolution of new protein functions

(2010) Misha Soskine et al.   NATURE REVIEWS GENETICS

The protein kingdom extended: Ordered and intrinsically disordered proteins, their folding, supramolecular complex formation, and aggregation

(2010) Konstantin K. Turoverov et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Exploring the factors determining the dynamics of different protein folds

(2010) S. M. Hollup et al.   PROTEIN SCIENCE

Role of conformational sampling in computing mutation-induced changes in protein structure and stability

(2010) Elizabeth H. Kellogg et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The evolution and evolutionary consequences of marginal thermostability in proteins

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

Mutational Robustness of Ribosomal Protein Genes

(2010) P. A. Lind et al.   SCIENCE

Quantifying the Impact of Dependent Evolution among Sites in Phylogenetic Inference

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

The Effect of Sequence Evolution on Protein Structural Divergence

(2009) Simon G. Williams et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparing Models of Evolution for Ordered and Disordered Proteins

(2009) C. J. Brown et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

A sequence-compatible amount of native burial information is sufficient for determining the structure of small globular proteins

(2009) Antonio F. Pereira de Araujo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The continuity of protein structure space is an intrinsic property of proteins

(2009) J. Skolnick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Posttranslational regulation impacts the fate of duplicated genes

(2009) G. D. Amoutzias et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Physicochemical principles that regulate the competition between functional and dysfunctional association of proteins

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

A perturbative view of protein structural variation

(2009) Julián Echave et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Cross-Over between Discrete and Continuous Protein Structure Space: Insights into Automatic Classification and Networks of Protein Structures

(2009) Alberto Pascual-García et al.   PLoS Computational Biology

The Protein Folding Problem

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

The unfoldomics decade: an update on intrinsically disordered proteins

(2008) A Keith Dunker et al.   BMC GENOMICS

Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution

(2008) D. Allan Drummond et al.   CELL

The structure of protein evolution and the evolution of protein structure

(2008) Richard A Goldstein   CURRENT OPINION IN STRUCTURAL BIOLOGY

Evolutionary conservation of protein vibrational dynamics

(2008) Sandra Maguid et al.   GENE

Site-Specific Unfolding Thermodynamics of a Helix-Turn-Helix Protein

(2008) Krista E. Amunson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

How Protein Stability and New Functions Trade Off

(2008) Nobuhiko Tokuriki et al.   PLoS Computational Biology