AIMC Topic: Protein Interaction Domains and Motifs

Clear Filters Showing 21 to 30 of 59 articles

Exploring the potential of 3D Zernike descriptors and SVM for protein-protein interface prediction.

BMC bioinformatics Feb 6, 2018
BACKGROUND: The correct determination of protein-protein interaction interfaces is important for understanding disease mechanisms and for rational drug design. To date, several computational methods for the prediction of protein interfaces have been ...
Area Under Curve Amino Acids ROC Curve Binding Sites Support Vector Machine Protein Interaction Domains and Motifs Proteins
View on PubMed DOI

InfAcrOnt: calculating cross-ontology term similarities using information flow by a random walk.

BMC genomics Jan 19, 2018
BACKGROUND: Since the establishment of the first biomedical ontology Gene Ontology (GO), the number of biomedical ontology has increased dramatically. Nowadays over 300 ontologies have been built including extensively used Disease Ontology (DO) and H...
Models, Biological Yeasts Gene Ontology Protein Interaction Domains and Motifs Gene Regulatory Networks Genomics Computational Biology Software Gene Expression Profiling Humans
View on PubMed DOI

Protein structure modeling and refinement by global optimization in CASP12.

Proteins Dec 5, 2017
For protein structure modeling in the CASP12 experiment, we have developed a new protocol based on our previous CASP11 approach. The global optimization method of conformational space annealing (CSA) was applied to 3 stages of modeling: multiple sequ...
Humans Machine Learning Algorithms Computational Biology Protein Conformation Protein Folding Sequence Analysis, Protein Protein Interaction Domains and Motifs Models, Molecular Molecular Dynamics Simulation Crystallography, X-Ray Support Vector Machine Models, Statistical Proteins
View on PubMed DOI

Simultaneous refinement of inaccurate local regions and overall structure in the CASP12 protein model refinement experiment.

Proteins Oct 26, 2017
Advances in protein model refinement techniques are required as diverse sources of protein structure information are available from low-resolution experiments or informatics-based computations such as cryo-EM, NMR, homology models, or predicted resid...
Models, Molecular Molecular Dynamics Simulation Crystallography, X-Ray Algorithms Computational Biology Proteins Protein Conformation Sequence Analysis, Protein Protein Interaction Domains and Motifs Humans Machine Learning
View on PubMed DOI

Improved protein contact predictions with the MetaPSICOV2 server in CASP12.

Proteins Sep 29, 2017
In this paper, we present the results for the MetaPSICOV2 contact prediction server in the CASP12 community experiment (http://predictioncenter.org). Over the 35 assessed Free Modelling target domains the MetaPSICOV2 server achieved a mean precision ...
Crystallography, X-Ray Protein Conformation Protein Interaction Domains and Motifs Proteins Models, Molecular Internet Humans Neural Networks, Computer Algorithms Computational Biology Machine Learning Software
View on PubMed DOI

Protein-protein interaction site predictions with minimum covariance determinant and Mahalanobis distance.

Journal of theoretical biology Sep 1, 2017
Protein-protein interaction site (PPIS) prediction must deal with the diversity of interaction sites that limits their prediction accuracy. Use of proteins with unknown or unidentified interactions can also lead to missing interfaces. Such data error...
Artificial Intelligence Support Vector Machine Supervised Machine Learning Binding Sites Protein Interaction Domains and Motifs
View on PubMed DOI

Predicting the helix-helix interactions from correlated residue mutations.

Proteins Aug 24, 2017
Helix-helix interactions are crucial in the structure assembly, stability and function of helix-rich proteins including many membrane proteins. In spite of remarkable progresses over the past decades, the accuracy of predicting protein structures fro...
Machine Learning Protein Conformation, alpha-Helical Amino Acid Sequence Binding Sites Protein Interaction Domains and Motifs Protein Binding Computational Biology Membrane Proteins
View on PubMed DOI

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...
Mutation Humans Epitopes Neural Networks, Computer Ligands Databases, Protein Machine Learning Histocompatibility Antigens Class II Antibodies, Monoclonal Structure-Activity Relationship Binding Sites Peptides Protein Interaction Domains and Motifs Protein Binding Computational Biology
View on PubMed DOI

Machine Learning and Network Analysis of Molecular Dynamics Trajectories Reveal Two Chains of Red/Ox-specific Residue Interactions in Human Protein Disulfide Isomerase.

Scientific reports Jun 16, 2017
The human protein disulfide isomerase (hPDI), is an essential four-domain multifunctional enzyme. As a result of disulfide shuffling in its terminal domains, hPDI exists in two oxidation states with different conformational preferences which are impo...
Protein Interaction Mapping Humans Protein Disulfide-Isomerases Oxidation-Reduction Protein Interaction Domains and Motifs Machine Learning Molecular Dynamics Simulation Protein Interaction Maps Protein Conformation
View on PubMed DOI

Editorial-Sequences and topology.

Current opinion in structural biology Jun 4, 2017
Binding Sites Thermodynamics Protein Conformation, beta-Strand Protein Binding Protein Interaction Mapping Protein Multimerization Animals Humans Computational Biology Protein Interaction Domains and Motifs Machine Learning Molecular Docking Simulation Proteins Protein Conformation, alpha-Helical
View on PubMed DOI
Popular Topics
Recent Journals