AIMC Topic: Protein Interaction Mapping

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Deep Learning for Protein-Protein Interaction Site Prediction.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2021
Protein-protein interactions (PPIs) are central to cellular functions. Experimental methods for predicting PPIs are well developed but are time and resource expensive and suffer from high false-positive error rates at scale. Computational prediction ...
Deep Learning Proteins Protein Interaction Mapping Supervised Machine Learning
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Network Analysis of Integrin Adhesion Complexes.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2021
Cell-surface adhesion receptors mediate interactions with the extracellular matrix (ECM) to control many fundamental aspects of cell behavior, including cell migration, survival, and proliferation. Integrin adhesion receptors recruit structural and s...
Integrins Multiprotein Complexes Cell Adhesion Software Protein Interaction Mapping Animals Humans Cell Movement Actin Cytoskeleton Protein Binding Neural Networks, Computer Extracellular Matrix Computational Biology Proteome
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Improved Prediction of Protein-Protein Interaction Mapping on by Using Amino Acid Sequence Features in a Supervised Learning Framework.

Protein and peptide letters Jan 1, 2021
BACKGROUND: Protein-Protein Interaction (PPI) has emerged as a key role in the control of many biological processes including protein function, disease incidence, and therapy design. However, the identification of PPI by wet lab experiment is a chall...
Humans Proteins Amino Acid Sequence Protein Interaction Mapping Sequence Analysis, Protein Protein Interaction Maps Computational Biology Support Vector Machine
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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 Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Thermodynamics Mutation, Missense Protein Interaction Mapping Protein Binding Proteins Internet Crystallography, X-Ray Binding Sites Benchmarking Datasets as Topic Humans Machine Learning Software
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NetGO: improving large-scale protein function prediction with massive network information.

Nucleic acids research Jul 2, 2019
Automated function prediction (AFP) of proteins is of great significance in biology. AFP can be regarded as a problem of the large-scale multi-label classification where a protein can be associated with multiple gene ontology terms as its labels. Bas...
Benchmarking Plants Amino Acid Sequence Structure-Activity Relationship Models, Molecular Internet Sequence Alignment Sequence Homology, Amino Acid Sequence Analysis, Protein Prokaryotic Cells Molecular Sequence Annotation Gene Ontology Protein Interaction Mapping Humans Machine Learning Software Proteins Databases, Protein Animals Computational Biology
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Compound-protein interaction prediction with end-to-end learning of neural networks for graphs and sequences.

Bioinformatics (Oxford, England) Jan 15, 2019
MOTIVATION: In bioinformatics, machine learning-based methods that predict the compound-protein interactions (CPIs) play an important role in the virtual screening for drug discovery. Recently, end-to-end representation learning for discrete symbolic...
Neural Networks, Computer Drug Discovery Deep Learning Proteins Protein Interaction Mapping
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canSAR: update to the cancer translational research and drug discovery knowledgebase.

Nucleic acids research Jan 8, 2019
canSAR (http://cansar.icr.ac.uk) is a public, freely available, integrative translational research and drug discovery knowlegebase. canSAR informs researchers to help solve key bottlenecks in cancer translation and drug discovery. It integrates genom...
Databases, Pharmaceutical Knowledge Bases Protein Conformation Drug Discovery Protein Interaction Mapping Antineoplastic Agents Humans User-Computer Interface Neoplasms Translational Research, Biomedical
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Autophagy and Apoptosis Specific Knowledgebases-guided Systems Pharmacology Drug Research.

Current cancer drug targets Jan 1, 2019
BACKGROUND: Autophagy and apoptosis are the basic physiological processes in cells that clean up aged and mutant cellular components or even the entire cells. Both autophagy and apoptosis are disrupted in most major diseases such as cancer and neurol...
Apoptosis Autophagy Knowledge Bases Computational Biology Signal Transduction Drug Development Molecular Docking Simulation Humans Protein Interaction Mapping Antineoplastic Agents Neoplasms
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Targeting Virus-host Protein Interactions: Feature Extraction and Machine Learning Approaches.

Current drug metabolism Jan 1, 2019
BACKGROUND: Targeting critical viral-host Protein-Protein Interactions (PPIs) has enormous application prospects for therapeutics. Using experimental methods to evaluate all possible virus-host PPIs is labor-intensive and time-consuming. Recent growt...
Algorithms Proteins Host-Pathogen Interactions Humans Viruses Machine Learning Protein Interaction Mapping
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Prediction of human-Bacillus anthracis protein-protein interactions using multi-layer neural network.

Bioinformatics (Oxford, England) Dec 15, 2018
MOTIVATION: Triplet amino acids have successfully been included in feature selection to predict human-HPV protein-protein interactions (PPI). The utility of supervised learning methods is curtailed due to experimental data not being available in suff...
Bacterial Proteins Support Vector Machine Humans Protein Interaction Mapping Proteins Neural Networks, Computer Bacillus anthracis Models, Molecular Computational Biology
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