AIMC Topic: Models, Molecular

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Rapid Design of Knowledge-Based Scoring Potentials for Enrichment of Near-Native Geometries in Protein-Protein Docking.

PloS one Jan 24, 2017
Protein-protein docking protocols aim to predict the structures of protein-protein complexes based on the structure of individual partners. Docking protocols usually include several steps of sampling, clustering, refinement and re-scoring. The scorin...
Computer Simulation Molecular Docking Simulation Protein Binding Software Algorithms Linear Models Protein Conformation Monte Carlo Method Protein Interaction Mapping Models, Molecular Models, Chemical Knowledge Bases
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Protein sequence-similarity search acceleration using a heuristic algorithm with a sensitive matrix.

Journal of structural and functional genomics Jan 12, 2017
Protein database search for public databases is a fundamental step in the target selection of proteins in structural and functional genomics and also for inferring protein structure, function, and evolution. Most database search methods employ amino ...
Algorithms Models, Molecular Sequence Alignment Sequence Analysis, Protein Computer Heuristics Computational Biology Proteins Databases, Protein
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A novel sandwich-type electrochemical immunosensor for PSA detection based on PtCu bimetallic hybrid (2D/2D) rGO/g-CN.

Biosensors & bioelectronics Dec 31, 2016
In this work, a sensitive sandwich-type electrochemical immunosensor was designed for the quantitative detection of prostate-specific antigen (PSA) by amperometric i-t. The Au loaded on thionine functionalized graphene oxide (Au@Th/GO) was used as a ...
Gold Humans Nitriles Reproducibility of Results Copper Limit of Detection Hydrogen Peroxide Biosensing Techniques Prostate-Specific Antigen Platinum Models, Molecular Graphite Electrochemical Techniques
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An ensemble micro neural network approach for elucidating interactions between zinc finger proteins and their target DNA.

BMC genomics Dec 22, 2016
BACKGROUND: The ability to engineer zinc finger proteins binding to a DNA sequence of choice is essential for targeted genome editing to be possible. Experimental techniques and molecular docking have been successful in predicting protein-DNA interac...
Molecular Conformation DNA Neural Networks, Computer Binding Sites Models, Molecular Zinc Fingers Algorithms DNA-Binding Proteins Protein Binding
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Beyond Rotatable Bond Counts: Capturing 3D Conformational Flexibility in a Single Descriptor.

Journal of chemical information and modeling Dec 6, 2016
A new molecular descriptor, nConf, based on chemical connectivity, is presented which captures the accessible conformational space of a molecule. Currently the best available two-dimensional descriptors for quantifying the flexibility of a particular...
Models, Molecular Machine Learning Crystallization Algorithms Molecular Conformation Drug Design
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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...
Protein Structure, Tertiary Neural Networks, Computer Machine Learning Algorithms Models, Molecular Data Accuracy 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...
Protein Interaction Domains and Motifs Arabidopsis Molecular Sequence Annotation Gene Ontology Protein Interaction Mapping Models, Molecular Data Mining High-Throughput Nucleotide Sequencing Datasets as Topic Saccharomyces cerevisiae Drosophila melanogaster Support Vector Machine Escherichia coli Proteins Animals Mice Computational Biology Humans Computer Simulation
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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...
Machine Learning Models, Molecular Quantum Theory Molecular Conformation Thermodynamics
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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 Databases, Protein Magnetic Resonance Spectroscopy Humans Models, Molecular Inhibitory Concentration 50 HIV Envelope Protein gp120 Antibodies, Neutralizing Neural Networks, Computer Crystallography, X-Ray HIV Infections
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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...
Protein Structure, Secondary Models, Molecular Heme Binding Sites Protein Binding Computational Biology Databases, Protein Machine Learning Software Algorithms
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