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FFLUX: Transferability of polarizable machine-learned electrostatics in peptide chains.

Journal of computational chemistry Mar 10, 2017
The fully polarizable, multipolar, and atomistic force field protein FFLUX is being built from machine learning (i.e., kriging) models, each of which predicts an atomic property. Each atom of a given protein geometry needs to be assigned such a krigi...
Thermodynamics Physical Phenomena Amino Acids Protein Conformation Static Electricity Machine Learning Peptides Models, Theoretical Proteins Models, Molecular
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Crystal Structure Representation for Neural Networks using Topological Approach.

Molecular informatics Mar 7, 2017
In the present work we describe a new approach, which uses topology of crystals for physicochemical properties prediction using artificial neural networks (ANN). The topologies of 268 crystal structures were determined using ToposPro software. Quotie...
Humans Models, Molecular Molecular Structure Entropy Neural Networks, Computer Software Algorithms
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Study of Structure-active Relationship for Inhibitors of HIV-1 Integrase LEDGF/p75 Interaction by Machine Learning Methods.

Molecular informatics Feb 28, 2017
HIV-1 integrase (IN) is a promising target for anti-AIDS therapy, and LEDGF/p75 is proved to enhance the HIV-1 integrase strand transfer activity in vitro. Blocking the interaction between IN and LEDGF/p75 is an effective way to inhibit HIV replicati...
HIV Integrase Reproducibility of Results Intercellular Signaling Peptides and Proteins ROC Curve HIV Integrase Inhibitors Humans Structure-Activity Relationship Molecular Conformation Protein Binding Machine Learning Models, Molecular Computer Simulation Molecular Structure
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A Hybrid Knowledge-Based and Empirical Scoring Function for Protein-Ligand Interaction: SMoG2016.

Journal of chemical information and modeling Feb 27, 2017
We present the third generation of our scoring function for the prediction of protein-ligand binding free energy. This function is now a hybrid between a knowledge-based potential and an empirical function. We constructed a diversified set of ∼1000 c...
Protein Binding Proteins Ligands Probability Protein Conformation Databases, Protein Models, Molecular Knowledge Bases Entropy
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Classifying kinase conformations using a machine learning approach.

BMC bioinformatics Feb 2, 2017
BACKGROUND: Signaling proteins such as protein kinases adopt a diverse array of conformations to respond to regulatory signals in signaling pathways. Perhaps the most fundamental conformational change of a kinase is the transition between active and ...
Protein Conformation Models, Molecular Machine Learning Protein Kinases Catalytic Domain
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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...
Monte Carlo Method Protein Interaction Mapping Protein Binding Models, Molecular Models, Chemical Knowledge Bases Linear Models Protein Conformation Algorithms Computer Simulation Software Molecular Docking Simulation
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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 ...
Sequence Analysis, Protein Computer Heuristics Databases, Protein Models, Molecular Sequence Alignment Computational Biology Proteins Algorithms
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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 ...
Electrochemical Techniques Humans Gold Reproducibility of Results Limit of Detection Graphite Prostate-Specific Antigen Hydrogen Peroxide Nitriles Copper Biosensing Techniques Platinum Models, Molecular
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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...
Protein Binding Neural Networks, Computer Zinc Fingers DNA-Binding Proteins DNA Algorithms Models, Molecular Molecular Conformation Binding Sites
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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...
Machine Learning Algorithms Drug Design Models, Molecular Crystallization Molecular Conformation
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