MOTIVATION: The Protein Data Bank (PDB), the ultimate source for data in structural biology, is inherently imbalanced. To alleviate biases, virtually all structural biology studies use nonredundant (NR) subsets of the PDB, which include only a fracti...
MOTIVATION: Protein secondary structure and backbone torsion angle prediction can provide important information for predicting protein 3D structures and protein functions. Our new methods MUFold-SS, MUFold-Angle, MUFold-BetaTurn and MUFold-GammaTurn,...
MOTIVATION: Messenger RNA subcellular localization mechanisms play a crucial role in post-transcriptional gene regulation. This trafficking is mediated by trans-acting RNA-binding proteins interacting with cis-regulatory elements called zipcodes. Whi...
MOTIVATION: Sequence-based prediction of one dimensional structural properties of proteins has been a long-standing subproblem of protein structure prediction. Recently, prediction accuracy has been significantly improved due to the rapid expansion o...
MOTIVATION: Domain boundary prediction is one of the most important problems in the study of protein structure and function. Many sequence-based domain boundary prediction methods are either template-based or machine learning (ML) based. ML-based met...
Journal of bioinformatics and computational biology
Oct 1, 2018
Protein secondary structure prediction (PSSP) is an important research field in bioinformatics. The representation of protein sequence features could be treated as a matrix, which includes the amino-acid residue (time-step) dimension and the feature ...
ComplexContact (http://raptorx2.uchicago.edu/ComplexContact/) is a web server for sequence-based interfacial residue-residue contact prediction of a putative protein complex. Interfacial residue-residue contacts are critical for understanding how pro...
MOTIVATION: Template-based modeling, including homology modeling and protein threading, is a popular method for protein 3D structure prediction. However, alignment generation and template selection for protein sequences without close templates remain...
Protein secondary structure prediction began in 1951 when Pauling and Corey predicted helical and sheet conformations for protein polypeptide backbone even before the first protein structure was determined. Sixty-five years later, powerful new method...
MOTIVATION: Methods able to provide reliable protein alignments are crucial for many bioinformatics applications. In the last years many different algorithms have been developed and various kinds of information, from sequence conservation to secondar...
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