MRFalign: Protein Homology Detection through Alignment of Markov Random Fields

Protein threading using context-specific alignment potential

(2013) J. Ma et al.   BIOINFORMATICS

Predicting protein contact map using evolutionary and physical constraints by integer programming

(2013) Z. Wang et al.   BIOINFORMATICS

A large-scale evaluation of computational protein function prediction

(2013) Predrag Radivojac et al.   NATURE METHODS

SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone

(2012) N. M. Daniels et al.   BIOINFORMATICS

A conditional neural fields model for protein threading

(2012) Jianzhu Ma et al.   BIOINFORMATICS

Discriminative modelling of context-specific amino acid substitution probabilities

(2012) Christof Angermüller et al.   BIOINFORMATICS

A Position-Specific Distance-Dependent Statistical Potential for Protein Structure and Functional Study

(2012) Feng Zhao et al.   STRUCTURE

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

(2011) David T. Jones et al.   BIOINFORMATICS

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

(2011) Michael Remmert et al.   NATURE METHODS

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Comparison of sequence profiles. Strategies for structural predictions using sequence information

(2010) Leszek Rychlewski et al.   PROTEIN SCIENCE

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Multiple Sequence Alignment Based on Profile Alignment of Intermediate Sequences

(2008) Yue Lu et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Matt: Local Flexibility Aids Protein Multiple Structure Alignment

(2008) Matthew Menke et al.   PLoS Computational Biology