Bayesian nonparametrics in protein remote homology search

Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative

(2014) K. Khafizov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ECOD: An Evolutionary Classification of Protein Domains

(2014) Hua Cheng et al.   PLoS Computational Biology

Dirichlet Mixtures, the Dirichlet Process, and the Structure of Protein Space

(2013) Viet-An Nguyen et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Activities at the Universal Protein Resource (UniProt)

(2013)   NUCLEIC ACIDS RESEARCH

SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures

(2013) Naomi K. Fox et al.   NUCLEIC ACIDS RESEARCH

CASP10 results compared to those of previous CASP experiments

(2013) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

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

Protein Modeling: What Happened to the “Protein Structure Gap”?

(2013) Torsten Schwede   STRUCTURE

A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction

(2013) Renxiang Yan et al.   Scientific Reports

Protein sequence comparison and fold recognition: progress and good-practice benchmarking

(2011) Johannes Söding et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

FFAS server: novel features and applications

(2011) L. Jaroszewski et al.   NUCLEIC ACIDS RESEARCH

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparison

(2010) Mindaugas Margelevičius et al.   BMC BIOINFORMATICS

I-TASSER: a unified platform for automated protein structure and function prediction

(2010) Ambrish Roy et al.   Nature Protocols

Homologous over-extension: a challenge for iterative similarity searches

(2010) Mileidy W. Gonzalez et al.   NUCLEIC ACIDS RESEARCH

Discrete–continuous duality of protein structure space

(2009) Ruslan I Sadreyev et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Sequence context-specific profiles for homology searching

(2009) A. Biegert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The use of automatic tools and human expertise in template-based modeling of CASP8 target proteins

(2009) Česlovas Venclovas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Searching protein structure databases with DaliLite v.3

(2008) L. Holm et al.   BIOINFORMATICS

PSI-BLAST pseudocounts and the minimum description length principle

(2008) Stephen F. Altschul et al.   NUCLEIC ACIDS RESEARCH