AI Medical Compendium Topic:
Protein Binding

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CGBVS-DNN: Prediction of Compound-protein Interactions Based on Deep Learning.

Molecular informatics Aug 12, 2016
Computational prediction of compound-protein interactions (CPIs) is of great importance for drug design as the first step in in-silico screening. We previously proposed chemical genomics-based virtual screening (CGBVS), which predicts CPIs by using a...
Proteome Binding Sites Machine Learning Software Molecular Docking Simulation Protein Binding
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Improving protein-protein interactions prediction accuracy using protein evolutionary information and relevance vector machine model.

Protein science : a publication of the Protein Society Aug 9, 2016
Predicting protein-protein interactions (PPIs) is a challenging task and essential to construct the protein interaction networks, which is important for facilitating our understanding of the mechanisms of biological systems. Although a number of high...
Bacterial Proteins Helicobacter pylori Saccharomyces cerevisiae Saccharomyces cerevisiae Proteins Algorithms Protein Binding Support Vector Machine Databases, Protein
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Molecular Properties of Drugs Interacting with SLC22 Transporters OAT1, OAT3, OCT1, and OCT2: A Machine-Learning Approach.

The Journal of pharmacology and experimental therapeutics Aug 3, 2016
Statistical analysis was performed on physicochemical descriptors of ∼250 drugs known to interact with one or more SLC22 "drug" transporters (i.e., SLC22A6 or OAT1, SLC22A8 or OAT3, SLC22A1 or OCT1, and SLC22A2 or OCT2), followed by application of ma...
Substrate Specificity Organic Anion Transport Protein 1 Machine Learning Organic Anion Transporters, Sodium-Independent Protein Binding Organic Cation Transporter 1 Hydrogen-Ion Concentration Computational Biology Membrane Transport Proteins Models, Molecular Protein Conformation Pharmaceutical Preparations
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GGIP: Structure and sequence-based GPCR-GPCR interaction pair predictor.

Proteins Jun 8, 2016
G Protein-Coupled Receptors (GPCRs) are important pharmaceutical targets. More than 30% of currently marketed pharmaceutical medicines target GPCRs. Numerous studies have reported that GPCRs function not only as monomers but also as homo- or hetero-d...
Animals ROC Curve Protein Binding Mice Humans Area Under Curve Models, Molecular Amino Acid Sequence Binding Sites Support Vector Machine Databases, Protein Receptors, G-Protein-Coupled Protein Structure, Secondary Protein Multimerization Protein Interaction Domains and Motifs
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Effect of Binding Pose and Modeled Structures on SVMGen and GlideScore Enrichment of Chemical Libraries.

Journal of chemical information and modeling May 24, 2016
Virtual screening consists of docking libraries of small molecules to a target protein followed by rank-ordering of the resulting structures using scoring functions. The ability of scoring methods to distinguish between actives and inactives depends ...
Crystallography, X-Ray Small Molecule Libraries Molecular Docking Simulation Support Vector Machine User-Computer Interface Drug Evaluation, Preclinical Protein Binding Protein Kinases Ligands
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Toward High-Throughput Predictive Modeling of Protein Binding/Unbinding Kinetics.

Journal of chemical information and modeling May 20, 2016
One of the unaddressed challenges in drug discovery is that drug potency determined in vitro is not a reliable indicator of drug activity in vivo. Accumulated evidence suggests that in vivo activity is more strongly correlated with the binding/unbind...
Ligands Protein Conformation Static Electricity Thermodynamics Kinetics Molecular Dynamics Simulation Safety Machine Learning Drug Discovery Protein Binding Computational Biology
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g:Profiler-a web server for functional interpretation of gene lists (2016 update).

Nucleic acids research Apr 20, 2016
Functional enrichment analysis is a key step in interpreting gene lists discovered in diverse high-throughput experiments. g:Profiler studies flat and ranked gene lists and finds statistically significant Gene Ontology terms, pathways and other gene ...
Internet Plants Fungi Insecta Gene Expression Regulation Molecular Sequence Annotation Gene Ontology Gene Expression Profiling User-Computer Interface Protein Binding Transcription Factors Humans Animals Binding Sites Computer Graphics Vertebrates
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Deciphering the Complexity of Ligand-Protein Recognition Pathways Using Supervised Molecular Dynamics (SuMD) Simulations.

Journal of chemical information and modeling Apr 14, 2016
Molecular recognition is a crucial issue when aiming to interpret the mechanism of known active substances as well as to develop novel active candidates. Unfortunately, simulating the binding process is still a challenging task because it requires cl...
Ligands Cell Membrane Protein Conformation Protein Binding Receptors, G-Protein-Coupled Molecular Dynamics Simulation Supervised Machine Learning
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The Virtual Screening of the Drug Protein with a Few Crystal Structures Based on the Adaboost-SVM.

Computational and mathematical methods in medicine Apr 3, 2016
Using the theory of machine learning to assist the virtual screening (VS) has been an effective plan. However, the quality of the training set may reduce because of mixing with the wrong docking poses and it will affect the screening efficiencies. To...
Chemistry, Pharmaceutical Hydrogen Cathepsin K Binding Sites Ligands Crystallization Protein Conformation Combinatorial Chemistry Techniques Protein Binding Reproducibility of Results Models, Statistical Humans Computational Biology Proteins Software Databases, Protein Drug Design Support Vector Machine Algorithms Area Under Curve ROC Curve Imaging, Three-Dimensional
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Extracting drug-enzyme relation from literature as evidence for drug drug interaction.

Journal of biomedical semantics Mar 7, 2016
BACKGROUND: Information about drug-drug interactions (DDIs) is crucial for computational applications such as pharmacovigilance and drug repurposing. However, existing sources of DDIs have the problems of low coverage, low accuracy and low agreement....
Enzymes Pharmaceutical Preparations Machine Learning Drug Interactions Data Mining Protein Binding Biological Ontologies
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