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...
MOTIVATION: Protein contact prediction is important for protein structure and functional study. Both evolutionary coupling (EC) analysis and supervised machine learning methods have been developed, making use of different information sources. However...
MOTIVATION: Predicting the structure of protein loops is very challenging, mainly because they are not necessarily subject to strong evolutionary pressure. This implies that, unlike the rest of the protein, standard homology modeling techniques are n...
MOTIVATION: Protein fold space is a conceptual framework where all possible protein folds exist and ideas about protein structure, function and evolution may be analyzed. Classification of protein folds in this space is commonly achieved by using sim...
Journal of computational biology : a journal of computational molecular cell biology
Jul 29, 2015
Predicting the three-dimensional native structures of protein dimers, a problem known as protein-protein docking, is key to understanding molecular interactions. Docking is a computationally challenging problem due to the diversity of interactions an...
Databases of curated biomedical knowledge, such as the protein-locations reflected in the UniProtKB database, provide an accurate and useful resource to researchers and decision makers. Our goal is to augment the manual efforts currently used to cura...
Identifying the genes that cause disease is one of the most challenging issues to establish the diagnosis and treatment quickly. Several interesting methods have been introduced for disease gene identification for a decade. In general, the main diffe...
Alternative splicing acts on transcripts from almost all human multi-exon genes. Notwithstanding its ubiquity, fundamental ramifications of splicing on protein expression remain unresolved. The number and identity of spliced transcripts that form sta...
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...
BACKGROUND: High throughput sequencing technologies are able to identify the whole genomic variation of an individual. Gene-targeted and whole-exome experiments are mainly focused on coding sequence variants related to a single or multiple nucleotide...
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