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Binding Sites

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EMQIT: a machine learning approach for energy based PWM matrix quality improvement.

Biology direct Aug 1, 2017
BACKGROUND: Transcription factor binding affinities to DNA play a key role for the gene regulation. Learning the specificity of the mechanisms of binding TFs to DNA is important both to experimentalists and theoreticians. With the development of high...
Machine Learning Software ROC Curve Datasets as Topic Gene Expression Regulation Binding Sites Position-Specific Scoring Matrices Computational Biology Models, Genetic Transcription Factors Models, Molecular
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In silico identification of milk antihypertensive di- and tripeptides involved in angiotensin I-converting enzyme inhibitory activity.

Nutrition research (New York, N.Y.) Jul 28, 2017
Identification of bioactive milk peptides could improve food technology through improved selection of food supplements with a focus on antihypertensive properties. We hypothesized that angiotensin I-converting enzyme (ACE) inhibitory activities of mi...
Humans Animals Molecular Docking Simulation Milk Proteins Peptidyl-Dipeptidase A Proteolysis Binding Sites Hydrophobic and Hydrophilic Interactions Expert Systems Angiotensin-Converting Enzyme Inhibitors Antihypertensive Agents Catalytic Domain Cattle Quantitative Structure-Activity Relationship Models, Molecular Computational Biology Oligopeptides Protein Conformation Peptide Fragments Dietary Supplements Hydrogen Bonding Dipeptides
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Machine learning reveals a non-canonical mode of peptide binding to MHC class II molecules.

Immunology Jun 19, 2017
MHC class II molecules play a fundamental role in the cellular immune system: they load short peptide fragments derived from extracellular proteins and present them on the cell surface. It is currently thought that the peptide binds lying more or les...
Databases, Protein Antibodies, Monoclonal Structure-Activity Relationship Mutation Peptides Protein Binding Computational Biology Histocompatibility Antigens Class II Epitopes Ligands Binding Sites Protein Interaction Domains and Motifs Humans Neural Networks, Computer Machine Learning
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Editorial-Sequences and topology.

Current opinion in structural biology Jun 4, 2017
Protein Multimerization Protein Interaction Domains and Motifs Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Humans Proteins Machine Learning Binding Sites Animals Thermodynamics Protein Interaction Mapping Molecular Docking Simulation Protein Binding Computational Biology
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TIGERi: modeling and visualizing the responses to perturbation of a transcription factor network.

BMC bioinformatics May 31, 2017
BACKGROUND: Transcription factor (TF) networks play a key role in controlling the transfer of genetic information from gene to mRNA. Much progress has been made on understanding and reverse-engineering TF network topologies using a range of experimen...
Mice, Knockout Binding Sites Mitogen-Activated Protein Kinase 14 Transcriptome Gene Regulatory Networks Mice Transcription Factors Machine Learning Animals
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pDHS-SVM: A prediction method for plant DNase I hypersensitive sites based on support vector machine.

Journal of theoretical biology May 26, 2017
DNase I hypersensitive sites (DHSs) are accessible chromatin regions hypersensitive to cleavages by DNase I endonucleases. DHSs are indicative of cis-regulatory DNA elements (CREs), all of which play important roles in global gene expression regulati...
Algorithms Support Vector Machine Oryza Binding Sites Genome, Plant Arabidopsis Dinucleotide Repeats Regulatory Sequences, Nucleic Acid Deoxyribonuclease I
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Protein-Protein Interaction Interface Residue Pair Prediction Based on Deep Learning Architecture.

IEEE/ACM transactions on computational biology and bioinformatics May 19, 2017
MOTIVATION: Proteins usually fulfill their biological functions by interacting with other proteins. Although some methods have been developed to predict the binding sites of a monomer protein, these are not sufficient for prediction of the interactio...
Computational Biology Proteins Surface Properties Molecular Docking Simulation Protein Conformation Binding Sites Deep Learning Protein Binding
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Discriminating between HuR and TTP binding sites using the k-spectrum kernel method.

PloS one Mar 23, 2017
BACKGROUND: The RNA binding proteins (RBPs) human antigen R (HuR) and Tristetraprolin (TTP) are known to exhibit competitive binding but have opposing effects on the bound messenger RNA (mRNA). How cells discriminate between the two proteins is an in...
Catalytic Domain Humans Binding Sites Models, Theoretical ELAV-Like Protein 1 Support Vector Machine Tristetraprolin
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Staged heterogeneity learning to identify conformational B-cell epitopes from antigen sequences.

BMC genomics Mar 14, 2017
BACKGROUND: The broad heterogeneity of antigen-antibody interactions brings tremendous challenges to the design of a widely applicable learning algorithm to identify conformational B-cell epitopes. Besides the intrinsic heterogeneity introduced by di...
Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Epitope Mapping Humans Antigen-Antibody Complex Protein Binding Protein Interaction Domains and Motifs B-Lymphocytes Models, Statistical Epitopes, B-Lymphocyte Supervised Machine Learning Antigens Binding Sites
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Active learning for computational chemogenomics.

Future medicinal chemistry Mar 6, 2017
AIM: Computational chemogenomics models the compound-protein interaction space, typically for drug discovery, where existing methods predominantly either incorporate increasing numbers of bioactivity samples or focus on specific subfamilies of protei...
Binding Sites Machine Learning Proteins Models, Chemical Computer Simulation Ligands Drug Discovery Databases, Chemical Genomics Computational Biology
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