CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction

Finding optimal interaction interface alignments between biological complexes

(2015) Xuefeng Cui et al.   BIOINFORMATICS

A new method to improve network topological similarity search: applied to fold recognition

(2015) J. Lhota et al.   BIOINFORMATICS

Improving Protein Fold Recognition by Deep Learning Networks

(2015) Taeho Jo et al.   Scientific Reports

Global view of the protein universe

(2014) S. Nepomnyachiy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MRFalign: Protein Homology Detection through Alignment of Markov Random Fields

(2014) Jianzhu Ma et al.   PLoS Computational Biology

Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection

(2013) Bin Liu et al.   BIOINFORMATICS

The Protein Model Portal—a comprehensive resource for protein structure and model information

(2013) Juergen Haas et al.   Database-The Journal of Biological Databases and Curation

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

Protein domain recurrence and order can enhance prediction of protein functions

(2012) Mario Abdel Messih et al.   BIOINFORMATICS

Multiple graph regularized protein domain ranking

(2012) Jim Wang et al.   BMC BIOINFORMATICS

ProDis-ContSHC: learning protein dissimilarity measures and hierarchical context coherently for protein-protein comparison in protein database retrieval

(2012) Jingyan Wang et al.   BMC BIOINFORMATICS

Exhaustive and Efficient Constraint Propagation: A Graph-Based Learning Approach and Its Applications

(2012) Zhiwu Lu et al.   INTERNATIONAL JOURNAL OF COMPUTER VISION

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

Template-based protein structure modeling using the RaptorX web server

(2012) Morten Källberg et al.   Nature Protocols

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Detecting Remote Evolutionary Relationships among Proteins by Large-Scale Semantic Embedding

(2011) Iain Melvin et al.   PLoS Computational Biology

How significant is a protein structure similarity with TM-score = 0.5?

(2010) Jinrui Xu et al.   BIOINFORMATICS

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

(2010) Ambrish Roy et al.   Nature Protocols

Fast and accurate automatic structure prediction with HHpred

(2009) Andrea Hildebrand et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improving consensus contact prediction via server correlation reduction

(2009) Xin Gao et al.   BMC STRUCTURAL BIOLOGY

MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information

(2008) Sitao Wu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS