Rotamer libraries in the 21st century

RL Dunbrack Jr - Current opinion in structural biology, 2002 - Elsevier
Rotamer libraries are widely used in protein structure prediction, protein design, and
structure refinement. As the size of the structure data base has increased rapidly in recent …

Aurora A kinase (AURKA) in normal and pathological cell division

AS Nikonova, I Astsaturov, IG Serebriiskii… - Cellular and Molecular …, 2013 - Springer
Temporally and spatially controlled activation of the Aurora A kinase (AURKA) regulates
centrosome maturation, entry into mitosis, formation and function of the bipolar spindle, and …

Sequence comparison and protein structure prediction

RL Dunbrack Jr - Current opinion in structural biology, 2006 - Elsevier
Sequence comparison is a major step in the prediction of protein structure from existing
templates in the Protein Data Bank. The identification of potentially remote homologues to …

Bayesian statistical analysis of protein side‐chain rotamer preferences

RL Dunbrack Jr, FE Cohen - Protein science, 1997 - Wiley Online Library
We present a Bayesian statistical analysis of the conformations of side chains in proteins
from the Protein Data Bank. This is an extension of the backbone‐dependent rotamer library …

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins

AD MacKerell Jr, D Bashford, M Bellott… - The journal of …, 1998 - ACS Publications
New protein parameters are reported for the all-atom empirical energy function in the
CHARMM program. The parameter evaluation was based on a self-consistent approach …

Backbone-dependent rotamer library for proteins application to side-chain prediction

RL Dunbrack Jr, M Karplus - Journal of molecular biology, 1993 - Elsevier
A backbone-dependent rotamer library for amino acid side-chains is developed and used for
constructing protein side-chain conformations from the main-chain co-ordinates. The …

PISCES: a protein sequence culling server

G Wang, RL Dunbrack Jr - Bioinformatics, 2003 - academic.oup.com
PISCES is a public server for culling sets of protein sequences from the Protein Data Bank
(PDB) by sequence identity and structural quality criteria. PISCES can provide lists culled …

Improved prediction of protein side‐chain conformations with SCWRL4

GG Krivov, MV Shapovalov… - … Structure, Function, and …, 2009 - Wiley Online Library
Determination of side-chain conformations is an important step in protein structure prediction
and protein design. Many such methods have been presented, although only a small …

The Rosetta all-atom energy function for macromolecular modeling and design

RF Alford, A Leaver-Fay, JR Jeliazkov… - Journal of chemical …, 2017 - ACS Publications
Over the past decade, the Rosetta biomolecular modeling suite has informed diverse
biological questions and engineering challenges ranging from interpretation of low …

PONDR-FIT: a meta-predictor of intrinsically disordered amino acids

B Xue, RL Dunbrack, RW Williams, AK Dunker… - … et Biophysica Acta (BBA …, 2010 - Elsevier
Protein intrinsic disorder is becoming increasingly recognized in proteomics research. While
lacking structure, many regions of disorder have been associated with biological function …