AI Medical Compendium Topic:
Protein Binding

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A Graph Approach to Mining Biological Patterns in the Binding Interfaces.

Journal of computational biology : a journal of computational molecular cell biology Nov 28, 2016
Protein-RNA interactions play important roles in the biological systems. Searching for regular patterns in the Protein-RNA binding interfaces is important for understanding how protein and RNA recognize each other and bind to form a complex. Herein, ...
Binding Sites Computer Graphics Amino Acid Motifs Protein Interaction Domains and Motifs Data Mining Animals RNA Protein Conformation Molecular Docking Simulation Protein Binding Support Vector Machine Proteins Computational Biology RNA-Binding Proteins Humans
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Informing the Human Plasma Protein Binding of Environmental Chemicals by Machine Learning in the Pharmaceutical Space: Applicability Domain and Limits of Predictability.

Journal of chemical information and modeling Nov 3, 2016
The free fraction of a xenobiotic in plasma (F) is an important determinant of chemical adsorption, distribution, metabolism, elimination, and toxicity, yet experimental plasma protein binding data are scarce for environmentally relevant chemicals. T...
Blood Proteins Pharmaceutical Preparations Quantitative Structure-Activity Relationship Environment Humans Protein Binding Support Vector Machine
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Improved pan-specific prediction of MHC class I peptide binding using a novel receptor clustering data partitioning strategy.

HLA Oct 20, 2016
Pan-specific prediction of receptor-ligand interaction is conventionally done using machine-learning methods that integrates information about both receptor and ligand primary sequences. To achieve optimal performance using machine learning, dealing ...
Ligands Oligopeptides Binding Sites Protein Interaction Domains and Motifs Epitopes Alleles Histocompatibility Antigens Class I Pan troglodytes Structural Homology, Protein Macaca Gorilla gorilla Humans Machine Learning Software Mice Gene Expression Animals Protein Binding
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Machine Learning Approaches for Predicting Protein Complex Similarity.

Journal of computational biology : a journal of computational molecular cell biology Oct 17, 2016
Discriminating native-like structures from false positives with high accuracy is one of the biggest challenges in protein-protein docking. While there is an agreement on the existence of a relationship between various favorable intermolecular interac...
Humans Neural Networks, Computer Machine Learning Proteins Animals Protein Conformation Molecular Docking Simulation Protein Binding
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HEMEsPred: Structure-Based Ligand-Specific Heme Binding Residues Prediction by Using Fast-Adaptive Ensemble Learning Scheme.

IEEE/ACM transactions on computational biology and bioinformatics Oct 4, 2016
Heme is an essential biomolecule that widely exists in numerous extant organisms. Accurately identifying heme binding residues (HEMEs) is of great importance in disease progression and drug development. In this study, a novel predictor named HEMEsPre...
Heme Binding Sites Protein Structure, Secondary Computational Biology Databases, Protein Algorithms Models, Molecular Protein Binding Machine Learning Software
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Sequence-Based Prediction of Protein-Carbohydrate Binding Sites Using Support Vector Machines.

Journal of chemical information and modeling Sep 22, 2016
Carbohydrate-binding proteins play significant roles in many diseases including cancer. Here, we established a machine-learning-based method (called sequence-based prediction of residue-level interaction sites of carbohydrates, SPRINT-CBH) to predict...
Protein Binding Support Vector Machine Proteins Binding Sites Carbohydrate Metabolism Databases, Protein Carbohydrates Humans Molecular Docking Simulation ROC Curve
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Correcting the impact of docking pose generation error on binding affinity prediction.

BMC bioinformatics Sep 22, 2016
BACKGROUND: Pose generation error is usually quantified as the difference between the geometry of the pose generated by the docking software and that of the same molecule co-crystallised with the considered protein. Surprisingly, the impact of this e...
Ligands Molecular Docking Simulation Protein Conformation Humans Protein Binding Nuclear Proteins Software Transcription Factors Pyrazines
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Transfer String Kernel for Cross-Context DNA-Protein Binding Prediction.

IEEE/ACM transactions on computational biology and bioinformatics Sep 15, 2016
Through sequence-based classification, this paper tries to accurately predict the DNA binding sites of transcription factors (TFs) in an unannotated cellular context. Related methods in the literature fail to perform such predictions accurately, sinc...
Models, Statistical DNA DNA-Binding Proteins Animals Protein Binding Mice Computational Biology Humans Machine Learning Algorithms
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Combined thioflavin T-Congo red fluorescence assay for amyloid fibril detection.

Methods and applications in fluorescence Sep 6, 2016
Fluorescence represents one of the most powerful tools for the detection and structural characterization of the pathogenic protein aggregates, amyloid fibrils. The traditional approaches to the identification and quantification of amyloid fibrils are...
Thiazoles Benzothiazoles Congo Red Fluorescent Dyes Reproducibility of Results Kinetics Fluorescence Amyloid Protein Binding
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A D3R prospective evaluation of machine learning for protein-ligand scoring.

Journal of computer-aided molecular design Sep 3, 2016
We assess the performance of several machine learning-based scoring methods at protein-ligand pose prediction, virtual screening, and binding affinity prediction. The methods and the manner in which they were trained make them sufficiently diverse to...
Ligands Binding Sites HSP90 Heat-Shock Proteins Humans Molecular Docking Simulation Machine Learning Computational Biology Protein Binding Algorithms Proteins Prospective Studies
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