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Protein Interaction Domains and Motifs

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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 28623339
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...
Humans Machine Learning Molecular Dynamics Simulation Oxidation-Reduction Protein Conformation Protein Disulfide-Isomerases Protein Interaction Domains and Motifs Protein Interaction Mapping Protein Interaction Maps
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Predicting the helix-helix interactions from correlated residue mutations.

Proteins 28833538
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...
Amino Acid Sequence Binding Sites Computational Biology Machine Learning Membrane Proteins Protein Binding Protein Conformation, alpha-Helical Protein Interaction Domains and Motifs
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Improved protein contact predictions with the MetaPSICOV2 server in CASP12.

Proteins 28901583
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 ...
Algorithms Computational Biology Crystallography, X-Ray Humans Internet Machine Learning Models, Molecular Neural Networks, Computer Protein Conformation Protein Interaction Domains and Motifs Proteins Software
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Protein-protein interaction site predictions with minimum covariance determinant and Mahalanobis distance.

Journal of theoretical biology 28867223
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 Binding Sites Protein Interaction Domains and Motifs Supervised Machine Learning Support Vector Machine
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Simultaneous refinement of inaccurate local regions and overall structure in the CASP12 protein model refinement experiment.

Proteins 29044810
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...
Algorithms Computational Biology Crystallography, X-Ray Humans Machine Learning Models, Molecular Molecular Dynamics Simulation Protein Conformation Protein Interaction Domains and Motifs Proteins Sequence Analysis, Protein
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Protein structure modeling and refinement by global optimization in CASP12.

Proteins 29159837
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...
Algorithms Computational Biology Crystallography, X-Ray Humans Machine Learning Models, Molecular Models, Statistical Molecular Dynamics Simulation Protein Conformation Protein Folding Protein Interaction Domains and Motifs Proteins Sequence Analysis, Protein Support Vector Machine
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InfAcrOnt: calculating cross-ontology term similarities using information flow by a random walk.

BMC genomics 29363423
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...
Computational Biology Gene Expression Profiling Gene Ontology Gene Regulatory Networks Genomics Humans Models, Biological Protein Interaction Domains and Motifs Software Yeasts
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Exploring the potential of 3D Zernike descriptors and SVM for protein-protein interface prediction.

BMC bioinformatics 29409446
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 ...
Amino Acids Area Under Curve Binding Sites Protein Interaction Domains and Motifs Proteins ROC Curve Support Vector Machine
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ComplexContact: a web server for inter-protein contact prediction using deep learning.

Nucleic acids research 29790960
ComplexContact (http://raptorx2.uchicago.edu/ComplexContact/) is a web server for sequence-based interfacial residue-residue contact prediction of a putative protein complex. Interfacial residue-residue contacts are critical for understanding how pro...
Amino Acid Sequence Computational Biology Databases, Factual Deep Learning Escherichia coli Humans Internet Protein Interaction Domains and Motifs Protein Structure, Secondary Proteins Sequence Alignment Sequence Homology, Amino Acid Software Structural Homology, Protein
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High precision in protein contact prediction using fully convolutional neural networks and minimal sequence features.

Bioinformatics (Oxford, England) 29718112
MOTIVATION: In addition to substitution frequency data from protein sequence alignments, many state-of-the-art methods for contact prediction rely on additional sources of information, or features, of protein sequences in order to predict residue-res...
Algorithms Amino Acid Sequence Computational Biology Neural Networks, Computer Protein Interaction Domains and Motifs Proteins Sequence Alignment
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