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

Touring Protein Space with Matt

(2012) Noah Daniels et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

A multiple-template approach to protein threading

(2011) Jian Peng et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Recognition of beta-structural motifs using hidden Markov models trained with simulated evolution

(2010) A. Kumar et al.   BIOINFORMATICS

Markov random fields reveal an N-terminal double beta-propeller motif as part of a bacterial hybrid two-component sensor system

(2010) M. Menke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequence specificity, statistical potentials, and three-dimensional structure prediction with self-correcting distance geometry calculations of β-sheet formation in proteins

(2010) Hongyao Zhu et al.   PROTEIN SCIENCE

Augmented training of hidden Markov models to recognize remote homologs via simulated evolution

(2009) A. Kumar et al.   BIOINFORMATICS

Conditional Graphical Models for Protein Structural Motif Recognition

(2009) Yan Liu et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima

(2009) Y. Zhang et al.   SCIENCE

ROC analysis: applications to the classification of biological sequences and 3D structures

(2008) P. Sonego et al.   BRIEFINGS IN BIOINFORMATICS

Graphical Models of Residue Coupling in Protein Families

(2008) J. Thomas et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Matt: Local Flexibility Aids Protein Multiple Structure Alignment

(2008) Matthew Menke et al.   PLoS Computational Biology