AIMC Topic: Sequence Analysis, Protein
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GoFDR: A sequence alignment based method for predicting protein functions.
Methods (San Diego, Calif.)
Aug 12, 2015
In this study, we developed a method named GoFDR for predicting Gene Ontology (GO)-based protein functions. The input for GoFDR is simply a query sequence-based multiple sequence alignment (MSA) produced by PSI-BLAST. For each GO term annotated to th...
MetazSecKB: the human and animal secretome and subcellular proteome knowledgebase.
Database : the journal of biological databases and curation
Aug 8, 2015
The subcellular location of a protein is a key factor in determining the molecular function of the protein in an organism. MetazSecKB is a secretome and subcellular proteome knowledgebase specifically designed for metazoan, i.e. human and animals. Th...
Identification of Heat Shock Protein families and J-protein types by incorporating Dipeptide Composition into Chou's general PseAAC.
Computer methods and programs in biomedicine
Jul 22, 2015
Heat Shock Proteins (HSPs) are the substantial ingredients for cell growth and viability, which are found in all living organisms. HSPs manage the process of folding and unfolding of proteins, the quality of newly synthesized proteins and protecting ...
TPpred3 detects and discriminates mitochondrial and chloroplastic targeting peptides in eukaryotic proteins.
Bioinformatics (Oxford, England)
Jun 16, 2015
MOTIVATION: Molecular recognition of N-terminal targeting peptides is the most common mechanism controlling the import of nuclear-encoded proteins into mitochondria and chloroplasts. When experimental information is lacking, computational methods can...
All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences.
Proceedings of the National Academy of Sciences of the United States of America
Apr 9, 2015
Transmembrane β-barrels (TMBs) carry out major functions in substrate transport and protein biogenesis but experimental determination of their 3D structure is challenging. Encouraged by successful de novo 3D structure prediction of globular and α-hel...
Woods: A fast and accurate functional annotator and classifier of genomic and metagenomic sequences.
Genomics
Apr 8, 2015
Functional annotation of the gigantic metagenomic data is one of the major time-consuming and computationally demanding tasks, which is currently a bottleneck for the efficient analysis. The commonly used homology-based methods to functionally annota...
Machine learning assisted design of highly active peptides for drug discovery.
PLoS computational biology
Apr 7, 2015
The discovery of peptides possessing high biological activity is very challenging due to the enormous diversity for which only a minority have the desired properties. To lower cost and reduce the time to obtain promising peptides, machine learning ap...
KeBABS: an R package for kernel-based analysis of biological sequences.
Bioinformatics (Oxford, England)
Mar 25, 2015
KeBABS provides a powerful, flexible and easy to use framework for KE: rnel- B: ased A: nalysis of B: iological S: equences in R. It includes efficient implementations of the most important sequence kernels, also including variants that allow for tak...
Prediction of cancer proteins by integrating protein interaction, domain frequency, and domain interaction data using machine learning algorithms.
BioMed research international
Mar 17, 2015
Many proteins are known to be associated with cancer diseases. It is quite often that their precise functional role in disease pathogenesis remains unclear. A strategy to gain a better understanding of the function of these proteins is to make use of...
Prediction and analysis of quorum sensing peptides based on sequence features.
PloS one
Mar 17, 2015
Quorum sensing peptides (QSPs) are the signaling molecules used by the Gram-positive bacteria in orchestrating cell-to-cell communication. In spite of their enormous importance in signaling process, their detailed bioinformatics analysis is lacking. ...
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