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Models, Molecular

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DeepQA: improving the estimation of single protein model quality with deep belief networks.

BMC bioinformatics Dec 5, 2016
BACKGROUND: Protein quality assessment (QA) useful for ranking and selecting protein models has long been viewed as one of the major challenges for protein tertiary structure prediction. Especially, estimating the quality of a single protein model, w...
Neural Networks, Computer Machine Learning Models, Molecular Data Accuracy Protein Structure, Tertiary Algorithms Support Vector Machine Proteins
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Prediction of Protein-Protein Interactions by Evidence Combining Methods.

International journal of molecular sciences Nov 22, 2016
Most cellular functions involve proteins' features based on their physical interactions with other partner proteins. Sketching a map of protein-protein interactions (PPIs) is therefore an important inception step towards understanding the basics of c...
Computer Simulation Animals Mice Humans Arabidopsis Gene Ontology Protein Interaction Mapping Protein Interaction Domains and Motifs Computational Biology Escherichia coli Support Vector Machine Saccharomyces cerevisiae Proteins Data Mining Drosophila melanogaster Models, Molecular High-Throughput Nucleotide Sequencing Molecular Sequence Annotation Datasets as Topic
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Synergies Between Quantum Mechanics and Machine Learning in Reaction Prediction.

Journal of chemical information and modeling Oct 25, 2016
Machine learning (ML) and quantum mechanical (QM) methods can be used in two-way synergy to build chemical reaction expert systems. The proposed ML approach identifies electron sources and sinks among reactants and then ranks all source-sink pairs. T...
Molecular Conformation Thermodynamics Machine Learning Models, Molecular Quantum Theory
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Learning the Relationship between the Primary Structure of HIV Envelope Glycoproteins and Neutralization Activity of Particular Antibodies by Using Artificial Neural Networks.

International journal of molecular sciences Oct 11, 2016
The dependency between the primary structure of HIV envelope glycoproteins (ENV) and the neutralization data for given antibodies is very complicated and depends on a large number of factors, such as the binding affinity of a given antibody for a giv...
HIV-1 Inhibitory Concentration 50 Crystallography, X-Ray Models, Molecular Antibodies, Neutralizing Magnetic Resonance Spectroscopy HIV Envelope Protein gp120 Humans Neural Networks, Computer HIV Infections Databases, Protein
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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...
Binding Sites Protein Structure, Secondary Algorithms Protein Binding Computational Biology Databases, Protein Machine Learning Models, Molecular Software Heme
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Machine Learning Prediction of the Energy Gap of Graphene Nanoflakes Using Topological Autocorrelation Vectors.

ACS combinatorial science Sep 14, 2016
The possibility of band gap engineering in graphene opens countless new opportunities for application in nanoelectronics. In this work, the energy gaps of 622 computationally optimized graphene nanoflakes were mapped to topological autocorrelation ve...
Energy Transfer Molecular Structure Machine Learning Nanostructures Models, Molecular Graphite
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ROCS-derived features for virtual screening.

Journal of computer-aided molecular design Sep 8, 2016
Rapid overlay of chemical structures (ROCS) is a standard tool for the calculation of 3D shape and chemical ("color") similarity. ROCS uses unweighted sums to combine many aspects of similarity, yielding parameter-free models for virtual screening. I...
Pharmaceutical Preparations Models, Molecular Molecular Structure Machine Learning Algorithms Computer-Aided Design Drug Design
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Sorting protein decoys by machine-learning-to-rank.

Scientific reports Aug 17, 2016
Much progress has been made in Protein structure prediction during the last few decades. As the predicted models can span a broad range of accuracy spectrum, the accuracy of quality estimation becomes one of the key elements of successful protein str...
Machine Learning Algorithms Proteins Models, Molecular Protein Transport
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Chemogenomics knowledgebase and systems pharmacology for hallucinogen target identification-Salvinorin A as a case study.

Journal of molecular graphics & modelling Aug 8, 2016
Drug abuse is a serious problem worldwide. Recently, hallucinogens have been reported as a potential preventative and auxiliary therapy for substance abuse. However, the use of hallucinogens as a drug abuse treatment has potential risks, as the funda...
Databases, Chemical Models, Molecular Reproducibility of Results Diterpenes, Clerodane Genomics Knowledge Bases Hallucinogens
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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 Organic Anion Transporters, Sodium-Independent Organic Cation Transporter 1 Hydrogen-Ion Concentration Membrane Transport Proteins Protein Conformation Models, Molecular Pharmaceutical Preparations Machine Learning Protein Binding Computational Biology
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