G Protein-Coupled Receptors (GPCRs) are important pharmaceutical targets. More than 30% of currently marketed pharmaceutical medicines target GPCRs. Numerous studies have reported that GPCRs function not only as monomers but also as homo- or hetero-d...
Journal of chemical information and modeling
Mar 15, 2016
Accurate prediction of protein secondary structure remains a crucial step in most approaches to the protein-folding problem, yet the prediction of ordered secondary structure, specifically beta-strands, remains a challenge. We developed a consensus s...
IEEE/ACM transactions on computational biology and bioinformatics
Feb 11, 2016
Transmembrane β-barrels (TMBs) are one important class of membrane proteins that play crucial functions in the cell. Membrane proteins are difficult wet-lab targets of structural biology, which call for accurate computational prediction approaches. H...
Protein secondary structure (SS) prediction is important for studying protein structure and function. When only the sequence (profile) information is used as input feature, currently the best predictors can obtain ~80% Q3 accuracy, which has not been...
We introduce a new representation and feature extraction method for biological sequences. Named bio-vectors (BioVec) to refer to biological sequences in general with protein-vectors (ProtVec) for proteins (amino-acid sequences) and gene-vectors (Gene...
Intrinsically disordered proteins or, regions perform important biological functions through their dynamic conformations during binding. Thus accurate identification of these disordered regions have significant implications in proper annotation of fu...
Journal of chemical information and modeling
Oct 20, 2015
The α-helical transmembrane proteins constitute 25% of the entire human proteome space and are difficult targets in high-resolution wet-lab structural studies, calling for accurate computational predictors. We present a novel sequence-based method ca...
Here we present the results of residue-residue contact predictions achieved in CASP11 by the CONSIP2 server, which is based around our MetaPSICOV contact prediction method. On a set of 40 target domains with a median family size of around 40 effectiv...
Understanding which peptides and proteins have the potential to undergo amyloid formation and what driving forces are responsible for amyloid-like fiber formation and stabilization remains limited. This is mainly because proteins that can undergo str...
Direct prediction of protein structure from sequence is a challenging problem. An effective approach is to break it up into independent sub-problems. These sub-problems such as prediction of protein secondary structure can then be solved independentl...
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