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

A Roy, A Kucukural, Y Zhang - Nature protocols, 2010 - nature.com
The iterative threading assembly refinement (I-TASSER) server is an integrated platform for
automated protein structure and function prediction based on the sequence-to-structure-to …

General overview on structure prediction of twilight-zone proteins

BY Khor, GJ Tye, TS Lim, YS Choong - Theoretical Biology and Medical …, 2015 - Springer
Protein structure prediction from amino acid sequence has been one of the most challenging
aspects in computational structural biology despite significant progress in recent years …

Automated comparative protein structure modeling with SWISS‐MODEL and Swiss‐PdbViewer: A historical perspective

N Guex, MC Peitsch, T Schwede - Electrophoresis, 2009 - Wiley Online Library
SWISS‐MODEL pioneered the field of automated modeling as the first protein modeling
service on the Internet. In combination with the visualization tool Swiss‐PdbViewer, the …

FINDSITE: a combined evolution/structure-based approach to protein function prediction

J Skolnick, M Brylinski - Briefings in bioinformatics, 2009 - academic.oup.com
A key challenge of the post-genomic era is the identification of the function (s) of all the
molecules in a given organism. Here, we review the status of sequence and structure-based …

Fast and accurate automatic structure prediction with HHpred

A Hildebrand, M Remmert, A Biegert… - Proteins: Structure …, 2009 - Wiley Online Library
Automated protein structure prediction is becoming a mainstream tool for biological
research. This has been fueled by steady improvements of publicly available automated …

Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties …

Y Yang, E Faraggi, H Zhao, Y Zhou - Bioinformatics, 2011 - academic.oup.com
Motivation: In recent years, development of a single-method fold-recognition server lags
behind consensus and multiple template techniques. However, a good consensus …

Fast procedure for reconstruction of full‐atom protein models from reduced representations

P Rotkiewicz, J Skolnick - Journal of computational chemistry, 2008 - Wiley Online Library
We introduce PULCHRA, a fast and robust method for the reconstruction of full‐atom protein
models starting from a reduced protein representation. The algorithm is particularly suitable …

Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment

I Kufareva, M Rueda, V Katritch, RC Stevens… - Structure, 2011 - cell.com
The community-wide GPCR Dock assessment is conducted to evaluate the status of
molecular modeling and ligand docking for human G protein-coupled receptors. The present …

Nature of the protein universe

M Levitt - Proceedings of the National Academy of …, 2009 - National Acad Sciences
The protein universe is the set of all proteins of all organisms. Here, all currently known
sequences are analyzed in terms of families that have single-domain or multidomain …

pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination

A Lobley, MI Sadowski, DT Jones - Bioinformatics, 2009 - academic.oup.com
Motivation: Generation of structural models and recognition of homologous relationships for
unannotated protein sequences are fundamental problems in bioinformatics. Improving the …