AIMC Topic: Protein Interaction Domains and Motifs

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Protein-protein interaction site prediction through combining local and global features with deep neural networks.

Bioinformatics (Oxford, England) Feb 15, 2020
MOTIVATION: Protein-protein interactions (PPIs) play important roles in many biological processes. Conventional biological experiments for identifying PPI sites are costly and time-consuming. Thus, many computational approaches have been proposed to ...
Software Proteins Amino Acid Sequence Protein Interaction Domains and Motifs Neural Networks, Computer
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The PSIPRED Protein Analysis Workbench: 20 years on.

Nucleic acids research Jul 2, 2019
The PSIPRED Workbench is a web server offering a range of predictive methods to the bioscience community for 20 years. Here, we present the work we have completed to update the PSIPRED Protein Analysis Workbench and make it ready for the next 20 year...
Protein Interaction Domains and Motifs Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Amino Acid Sequence History, 21st Century Molecular Sequence Annotation Sequence Alignment Sequence Homology, Amino Acid Gene Ontology Binding Sites Proteins Models, Molecular Internet Software Protein Binding
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mCSM-PPI2: predicting the effects of mutations on protein-protein interactions.

Nucleic acids research Jul 2, 2019
Protein-protein Interactions are involved in most fundamental biological processes, with disease causing mutations enriched at their interfaces. Here we present mCSM-PPI2, a novel machine learning computational tool designed to more accurately predic...
Protein Interaction Domains and Motifs Thermodynamics Protein Conformation, alpha-Helical Mutation, Missense Protein Conformation, beta-Strand Protein Interaction Mapping Humans Machine Learning Software Benchmarking Protein Binding Datasets as Topic Proteins Crystallography, X-Ray Internet Binding Sites
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PrankWeb: a web server for ligand binding site prediction and visualization.

Nucleic acids research Jul 2, 2019
PrankWeb is an online resource providing an interface to P2Rank, a state-of-the-art method for ligand binding site prediction. P2Rank is a template-free machine learning method based on the prediction of local chemical neighborhood ligandability cent...
Binding Sites Thermodynamics Protein Interaction Domains and Motifs Amino Acid Sequence Ligands Datasets as Topic Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Humans Machine Learning Software Protein Binding Internet Proteins Benchmarking
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High precision in protein contact prediction using fully convolutional neural networks and minimal sequence features.

Bioinformatics (Oxford, England) Oct 1, 2018
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...
Protein Interaction Domains and Motifs Neural Networks, Computer Algorithms Amino Acid Sequence Sequence Alignment Computational Biology Proteins
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ComplexContact: a web server for inter-protein contact prediction using deep learning.

Nucleic acids research Jul 2, 2018
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...
Humans Software Databases, Factual Escherichia coli Proteins Deep Learning Computational Biology Structural Homology, Protein Sequence Alignment Sequence Homology, Amino Acid Internet Protein Interaction Domains and Motifs Amino Acid Sequence Protein Structure, Secondary
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ISPRED4: interaction sites PREDiction in protein structures with a refining grammar model.

Bioinformatics (Oxford, England) Jun 1, 2017
MOTIVATION: The identification of protein-protein interaction (PPI) sites is an important step towards the characterization of protein functional integration in the cell complexity. Experimental methods are costly and time-consuming and computational...
Protein Conformation Sequence Analysis, Protein Protein Interaction Domains and Motifs Machine Learning Software Computational Biology
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An Efficient Semi-supervised Learning Approach to Predict SH2 Domain Mediated Interactions.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2017
Src homology 2 (SH2) domain is an important subclass of modular protein domains that plays an indispensable role in several biological processes in eukaryotes. SH2 domains specifically bind to the phosphotyrosine residue of their binding peptides to ...
Computational Biology Signal Transduction Databases, Protein Algorithms Reproducibility of Results Protein Binding Humans Phosphotyrosine Workflow Web Browser Protein Interaction Domains and Motifs Supervised Machine Learning src Homology Domains Protein Interaction Mapping
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Protein-protein interaction site prediction in Homo sapiens and E. coli using an interaction-affinity based membership function in fuzzy SVM.

Journal of biosciences Oct 1, 2015
Protein-protein interaction (PPI) site prediction aids to ascertain the interface residues that participate in interaction processes. Fuzzy support vector machine (F-SVM) is proposed as an effective method to solve this problem, and we have shown tha...
Area Under Curve Escherichia coli Fuzzy Logic Gene Expression Databases, Protein Escherichia coli Proteins Protein Interaction Mapping Humans Protein Interaction Domains and Motifs Sensitivity and Specificity Support Vector Machine
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