Quantifying side-chain conformational variations in protein structure

Single-Point Mutation with a Rotamer Library Toolkit: Toward Protein Engineering

(2015) Joshua Pottel et al.   Journal of Chemical Information and Modeling

EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy

(2015) Benjamin A Barad et al.   NATURE METHODS

RNA-PuzzlesRound II: assessment of RNA structure prediction programs applied to three large RNA structures

(2015) Zhichao Miao et al.   RNA

How cryo-EM is revolutionizing structural biology

(2015) Xiao-chen Bai et al.   TRENDS IN BIOCHEMICAL SCIENCES

Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity

(2015) Noah Ollikainen et al.   PLoS Computational Biology

Too packed to change: side-chain packing and site-specific substitution rates in protein evolution

(2015) María Laura Marcos et al.   PeerJ

Backbone and side chain NMR assignment, along with the secondary structure prediction of RRM2 domain of La protein from a lower eukaryote exhibiting identical structural organization with its human homolog

(2014) Aikaterini I. Argyriou et al.   Biomolecular NMR Assignments

Improved packing of protein side chains with parallel ant colonies

(2014) Lijun Quan et al.   BMC BIOINFORMATICS

Protein side-chain modeling with a protein-dependent optimized rotamer library

(2014) Patricia Francis-Lyon et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Predicting the side-chain dihedral angle distributions of nonpolar, aromatic, and polar amino acids using hard sphere models

(2014) Alice Qinhua Zhou et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Backbone dependency further improves side chain prediction efficiency in the Energy-based Conformer Library (bEBL)

(2014) Sabareesh Subramaniam et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of protein side-chain conformation prediction methods in different residue environments

(2014) Lenna X. Peterson et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Residue-Specific Side-Chain Polymorphisms via Particle Belief Propagation

(2013) Laleh Soltan Ghoraie et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Design of a Rotamer Library for Coarse-Grained Models in Protein-Folding Simulations

(2013) María Larriva et al.   Journal of Chemical Information and Modeling

Critical assessment of methods of protein structure prediction (CASP) - round x

(2013) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein structure optimization by side-chain positioning via beta-complex

(2012) Joonghyun Ryu et al.   JOURNAL OF GLOBAL OPTIMIZATION

RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction

(2012) J. A. Cruz et al.   RNA

A Smoothed Backbone-Dependent Rotamer Library for Proteins Derived from Adaptive Kernel Density Estimates and Regressions

(2011) Maxim V. Shapovalov et al.   STRUCTURE

PHENIX: a comprehensive Python-based system for macromolecular structure solution

(2010) Paul D. Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Peripatetic proteins

(2010) Brian W. Matthews   PROTEIN SCIENCE

Automated electron-density sampling reveals widespread conformational polymorphism in proteins

(2010) P. Therese Lang et al.   PROTEIN SCIENCE