Incorporating post-translational modifications and unnatural amino acids into high-throughput modeling of protein structures

AMS 4.0: consensus prediction of post-translational modifications in protein sequences

(2012) Dariusz Plewczynski et al.   AMINO ACIDS

Expanding molecular modeling and design tools to non-natural sidechains

(2012) David Gfeller et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Incorporation of Noncanonical Amino Acids into Rosetta and Use in Computational Protein-Peptide Interface Design

(2012) P. Douglas Renfrew et al.   PLoS One

RASP: rapid modeling of protein side chain conformations

(2011) Zhichao Miao et al.   BIOINFORMATICS

Fast and accurate prediction of protein side-chain conformations

(2011) Shide Liang et al.   BIOINFORMATICS

A protein-dependent side-chain rotamer library

(2011) Md Shariful Bhuyan et al.   BMC BIOINFORMATICS

Data-Driven High-Throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress

(2011) Alessio Andronico et al.   Journal of Chemical Information and Modeling

PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse

(2011) P. V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

SIDEpro: A novel machine learning approach for the fast and accurate prediction of side-chain conformations

(2011) Ken Nagata et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2011) Maxim V. Shapovalov et al.   STRUCTURE

Open Babel: An open chemical toolbox

(2011) Noel M O'Boyle et al.   Journal of Cheminformatics

Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database

(2011) George A. Khoury et al.   Scientific Reports

PHOSIDA 2011: the posttranslational modification database

(2010) F. Gnad et al.   NUCLEIC ACIDS RESEARCH

The dynameomics rotamer library: Amino acid side chain conformations and dynamics from comprehensive molecular dynamics simulations in water

(2010) Alexander D. Scouras et al.   PROTEIN SCIENCE

Expanding the Genetic Code for Biological Studies

(2009) Qian Wang et al.   CHEMISTRY & BIOLOGY

Improved Prediction of Lysine Acetylation by Support Vector Machines

(2009) Songling Li et al.   PROTEIN AND PEPTIDE LETTERS

Improved prediction of protein side-chain conformations with SCWRL4

(2009) Georgii G. Krivov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Systematic study of protein sumoylation: Development of a site-specific predictor of SUMOsp 2.0

(2009) Jian Ren et al.   PROTEOMICS

Prediction of glycosylation sites using random forests

(2008) Stephen E Hamby et al.   BMC BIOINFORMATICS

A novel method for high accuracy sumoylation site prediction from protein sequences

(2008) Jialin Xu et al.   BMC BIOINFORMATICS

Meta-prediction of phosphorylation sites with weighted voting and restricted grid search parameter selection

(2008) Ji Wan et al.   NUCLEIC ACIDS RESEARCH

OPUS-Rota: A fast and accurate method for side-chain modeling

(2008) Mingyang Lu et al.   PROTEIN SCIENCE