AIMC Topic: Sequence Analysis, Protein

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Identifying DNA-binding proteins by combining support vector machine and PSSM distance transformation.

BMC systems biology Feb 6, 2015
BACKGROUND: DNA-binding proteins play a pivotal role in various intra- and extra-cellular activities ranging from DNA replication to gene expression control. Identification of DNA-binding proteins is one of the major challenges in the field of genome...
DNA-Binding Proteins Sequence Analysis, Protein Models, Molecular Nucleic Acid Conformation Computational Biology Amino Acid Sequence Protein Conformation Molecular Sequence Data Support Vector Machine Internet
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More challenges for machine-learning protein interactions.

Bioinformatics (Oxford, England) Jan 12, 2015
MOTIVATION: Machine learning may be the most popular computational tool in molecular biology. Providing sustained performance estimates is challenging. The standard cross-validation protocols usually fail in biology. Park and Marcotte found that even...
Artificial Intelligence Computational Biology Humans Sequence Analysis, Protein Saccharomyces cerevisiae Proteins Proteins Protein Interaction Mapping
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A Machine Learning Approach to Explain Drug Selectivity to Soluble and Membrane Protein Targets.

Molecular informatics Jan 8, 2015
Improved understanding of the forces that determine drug specificity to their targets is important for drug design and discovery, as well as for gaining knowledge about molecular recognition. Here, we present a machine learning approach that includes...
Machine Learning Membrane Proteins Sequence Analysis, Protein
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GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome.

Bioinformatics (Oxford, England) Jan 6, 2015
MOTIVATION: Glycosylation is a ubiquitous type of protein post-translational modification (PTM) in eukaryotic cells, which plays vital roles in various biological processes (BPs) such as cellular communication, ligand recognition and subcellular reco...
Glycosylation Protein Processing, Post-Translational Sequence Analysis, Protein Amino Acids Algorithms Artificial Intelligence Humans Proteome Software
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Identification of human drug targets using machine-learning algorithms.

Computers in biology and medicine Nov 20, 2014
Identification of potential drug targets is a crucial task in the drug-discovery pipeline. Successful identification of candidate drug targets in entire genomes is very useful, and computational prediction methods can speed up this process. In the cu...
Algorithms Drug Delivery Systems Sequence Analysis, Protein Humans Artificial Intelligence
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Prediction of β-lactamase and its class by Chou's pseudo-amino acid composition and support vector machine.

Journal of theoretical biology Oct 22, 2014
β-Lactam class of antibiotics is used as major therapeutic agent against a number of pathogenic microbes. The widespread and indiscriminate use of antibiotics to treat bacterial infection has prompted evolution of several evading mechanisms from the ...
Sequence Analysis, Protein beta-Lactams beta-Lactamases Protein Structure, Secondary Support Vector Machine Amino Acid Sequence Anti-Infective Agents
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Discrimination of acidic and alkaline enzyme using Chou's pseudo amino acid composition in conjunction with probabilistic neural network model.

Journal of theoretical biology Oct 22, 2014
Enzyme catalysis is one of the most essential and striking processes among of all the complex processes that have evolved in living organisms. Enzymes are biological catalysts, which play a significant role in industrial applications as well as in me...
Enzymes Sequence Analysis, Protein Models, Chemical Protein Folding Algorithms Databases, Protein Neural Networks, Computer
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PFP/ESG: automated protein function prediction servers enhanced with Gene Ontology visualization tool.

Bioinformatics (Oxford, England) Oct 1, 2014
UNLABELLED: Protein function prediction (PFP) is an automated function prediction method that predicts Gene Ontology (GO) annotations for a protein sequence using distantly related sequences and contextual associations of GO terms. Extended similarit...
Databases, Protein Molecular Sequence Annotation Computational Biology Humans Computer Graphics Proteins Gene Ontology Algorithms Sequence Analysis, Protein
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PseDNA-Pro: DNA-Binding Protein Identification by Combining Chou's PseAAC and Physicochemical Distance Transformation.

Molecular informatics Sep 26, 2014
Identification of DNA-binding proteins is an important problem in biomedical research as DNA-binding proteins are crucial for various cellular processes. Currently, the machine learning methods achieve the-state-of-the-art performance with different ...
Support Vector Machine Humans Databases, Protein Animals Sequence Analysis, Protein DNA-Binding Proteins
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MVSF-AB: accurate antibody-antigen binding affinity prediction via multi-view sequence feature learning.

Bioinformatics (Oxford, England) May 6, 2025
MOTIVATION: Predicting the binding affinity between antigens and antibodies accurately is crucial for assessing therapeutic antibody effectiveness and enhancing antibody engineering and vaccine design. Traditional machine learning methods have been w...
Algorithms Antibody Affinity Protein Binding Antibodies Sequence Analysis, Protein Antigens Antigen-Antibody Reactions Computational Biology Humans Machine Learning
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