Automated Procedure for Contact-Map-Based Protein Structure Reconstruction

Memoir: template-based structure prediction for membrane proteins

(2013) Jean-Paul Ebejer et al.   NUCLEIC ACIDS RESEARCH

Optimization of 3D Poisson-Nernst-Planck model for fast evaluation of diverse protein channels

(2013) Witold Dyrka et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

CASP10 results compared to those of previous CASP experiments

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

Assessment of CASP10 contact-assisted predictions

(2013) Todd J. Taylor et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

One contact for every twelve residues allows robust and accurate topology-level protein structure modeling

(2013) David E. Kim et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

(2012) Thomas A. Hopf et al.   CELL

Template-based protein structure modeling using the RaptorX web server

(2012) Morten Källberg et al.   Nature Protocols

Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis

(2012) T. Nugent et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

(2011) David T. Jones et al.   BIOINFORMATICS

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

Protein topology from predicted residue contacts

(2011) William R. Taylor et al.   PROTEIN SCIENCE

Evaluation of residue-residue contact predictions in CASP9

(2011) Bohdan Monastyrskyy et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Optimal contact definition for reconstruction of Contact Maps

(2010) Jose M Duarte et al.   BMC BIOINFORMATICS

Protein structure prediction on the Web: a case study using the Phyre server

(2009) Lawrence A Kelley et al.   Nature Protocols

Improved prediction of protein side-chain conformations with SCWRL4

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

Defining an Essence of Structure Determining Residue Contacts in Proteins

(2009) R. Sathyapriya et al.   PLoS Computational Biology

PConPy--a Python module for generating 2D protein maps

(2008) H. K. Ho et al.   BIOINFORMATICS

FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps

(2008) Marco Vassura et al.   BIOINFORMATICS

Ion flux through membrane channels-An enhanced algorithm for the Poisson-Nernst-Planck model

(2008) Witold Dyrka et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY