bioinformatics
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Wolf2Pack – Portal Based Atomistic
Force-Field Development

Wolf2Pack – Portal Based Atomistic<br/>Force-Field Development | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci300290g
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An In-Silico method for designing thermostable variant of a dimeric mesophilic protein based on its 3D structure

An In-Silico method for designing thermostable variant of a dimeric mesophilic protein based on its 3D structure | bioinformatics | Scoop.it
Available online 21 March 2013 Publication year: 2013 Source:Journal of Molecular Graphics and Modelling Designing proteins with enhanced thermostability has been a major interest of protein engineering because of its potential...
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Membrane Protein Modeling workshop to take place at the University of Chicago on May 7th

Membrane Protein Modeling workshop to take place at the University of Chicago on May 7th | bioinformatics | Scoop.it
During the week of the Membrane Protein Structural Dynamics Consortium (MPSDC)’s Annual Meeting, a workshop specifically dedicated to Membrane Protein Modeling will be held at the University of Chicago on Tuesday, May 7th.
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Mining basic active structures from a large-scale database

Background:
The Pubchem Database (pubchem.ncbi.nlm.nih.gov/) is a large-scale resource for chemical information, containing millions of chemical compound activities derived by high-throughput screening (HTS).
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Oversampling to Overcome Overfitting: Exploring the
Relationship between Data Set Composition, Molecular Descriptors,
and Predictive Modeling Methods

Oversampling to Overcome Overfitting: Exploring the<br/>Relationship between Data Set Composition, Molecular Descriptors,<br/>and Predictive Modeling Methods | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci4000536
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Optimization of molecular docking scores with support vector rank regression

Optimization of molecular docking scores with support vector rank regression | bioinformatics | Scoop.it
Abstract
This work introduces the support vector rank regression (SVRR) algorithm for the optimization of molecular docking scores. Seven original docking scores reported by two docking software were integrated by the SVRR algorithm.
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Computational phosphorylation site prediction in plants using random forests and organism-specific instance weights

Computational phosphorylation site prediction in plants using random forests and organism-specific instance weights | bioinformatics | Scoop.it
Motivation: Phosphorylation is the most important post-translational modification in eukaryotes.
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Fragment-Based Drug Discovery Using a Multidomain,
Parallel MD-MM/PBSA Screening Protocol

Journal of Chemical Information and ModelingDOI: 10.1021/ci300502h
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Pharmacophore Modeling, Homology Modeling, and in silico Screening Reveal Mammalian Target of Rapamycin Inhibitory Activities for Sotalol, Glyburide, Metipranolol, Sulfamethizole, Glipizide, and Pi...

Pharmacophore Modeling, Homology Modeling, and in silico Screening Reveal Mammalian Target of Rapamycin Inhibitory Activities for Sotalol, Glyburide, Metipranolol, Sulfamethizole, Glipizide, and Pi... | bioinformatics | Scoop.it
Available online 13 March 2013
Publication year: 2013
Source:Journal of Molecular Graphics and Modelling

Mammalian target of rapamycin (mTOR) is a serine/threonine kinase and member of the PI3K-related kinase (PIKK) family.
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Determination of the Potential of Drug Candidates to Cause Severe Skin Disorders Using Computational Modeling

Determination of the Potential of Drug Candidates to Cause Severe Skin Disorders Using Computational Modeling | bioinformatics | Scoop.it
Abstract
Efficient and accurate prediction for drugs’ potential to cause rare and severe adverse drug reactions (ADRs) is needed to facilitate the evaluation of risk-benefit ratio of drug candidates during drug development.
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Rendering Molecular Sketches for Publication Quality Output

Rendering Molecular Sketches for Publication Quality Output | bioinformatics | Scoop.it
Abstract The creation of 2D molecular structure diagrams that make full use of the capabilities of modern display systems, using only input data expressed in file formats used for cheminformatics, is a complex task that requires a number of...
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Encoding Protein–Ligand Interaction Patterns
in Fingerprints and Graphs

Encoding Protein–Ligand Interaction Patterns<br/>in Fingerprints and Graphs | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci300566n
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Algorithms of GPU-enabled reactive force field (ReaxFF) molecular dynamics

Algorithms of GPU-enabled reactive force field (ReaxFF) molecular dynamics | bioinformatics | Scoop.it
April 2013 Publication year: 2013 Source:Journal of Molecular Graphics and Modelling, Volume 41 Reactive force field (ReaxFF), a recent and novel bond order potential, allows for reactive molecular dynamics (ReaxFF MD) simulations...
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A3 Adenosine Receptor: Homology Modeling and 3D-Qsar Studies

A3 Adenosine Receptor: Homology Modeling and 3D-Qsar Studies | bioinformatics | Scoop.it
Available online 19 March 2013
Publication year: 2013
Source:Journal of Molecular Graphics and Modelling

Adenosine receptors (AR) belong to the superfamily of G-protein-coupled receptors (GPCRs).
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Discovery of a Novel Selective PPARγ Ligand
with Partial Agonist Binding Properties by Integrated in Silico/in Vitro Work Flow

Discovery of a Novel Selective PPARγ Ligand<br/>with Partial Agonist Binding Properties by Integrated in Silico/in Vitro Work Flow | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci3006148
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Antagonist binding and induced conformational dynamics of GPCR A2A adenosine receptor

Antagonist binding and induced conformational dynamics of GPCR A2A adenosine receptor | bioinformatics | Scoop.it
Abstract
The A2A adenosine receptor (A2AAR) is a unique G-protein coupled receptor (GPCR), because besides agonist, its antagonist could also lead to therapeutic relevance.
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ChemoPy: freely available python package for computational biology and chemoinformatics

ChemoPy: freely available python package for computational biology and chemoinformatics | bioinformatics | Scoop.it
Motivation: Molecular representation for small molecules has been routinely used in QSAR/SAR, virtual screening, database search, ranking, drug ADME/T prediction and other drug discovery processes.
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Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences

Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences | bioinformatics | Scoop.it
Abstract
Hot spot residues of proteins are fundamental interface residues that help proteins perform their functions. Detecting hot spots by experimental methods is costly and time-consuming.
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ChemoPy: freely available python package for computational biology and chemoinformatics

ChemoPy: freely available python package for computational biology and chemoinformatics | bioinformatics | Scoop.it
Motivation: Molecular representation for small molecules has been routinely used in QSAR/SAR, virtual screening, database search, ranking, drug ADME/T prediction and other drug discovery processes.
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PreDNA: accurate prediction of DNA-binding sites in proteins by integrating sequence and geometric structure information

Motivation: Protein–DNA interactions often take part in various crucial processes, which are essential for cellular function.
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Prediction of contact matrix for protein-protein interaction

Motivation: Prediction of protein–protein interaction has become an important part of systems biology in reverse engineering the biological networks for better understanding the molecular biology of the cell.
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Computational Investigation of SENP:SUMO Protein‒Protein Interaction for Structure Based Drug Design

Computational Investigation of SENP:SUMO Protein‒Protein Interaction for Structure Based Drug Design | bioinformatics | Scoop.it
Abstract
SUMO specific proteases (SENPs) are cysteine proteases that carry out the proteolytic processing of SUMO from its pro form as well as its deconjugation from substrate proteins.
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FTFlex: Accounting for binding site flexibility to improve fragment-based identification of druggable hot spots

FTFlex: Accounting for binding site flexibility to improve fragment-based identification of druggable hot spots | bioinformatics | Scoop.it
Computational solvent mapping finds binding hot spots, determines their druggability, and provides information for drug design.
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DNdisorder: predicting protein disorder using boosting and deep networks

Background:
A number of proteins contain regions which do not adopt a stable tertiary structure in their native state.
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Benchmarking of HPCC: A novel 3D molecular representation combining shape and pharmacophoric descriptors for efficient molecular similarity assessments

Benchmarking of HPCC: A novel 3D molecular representation combining shape and pharmacophoric descriptors for efficient molecular similarity assessments | bioinformatics | Scoop.it
April 2013 Publication year: 2013 Source:Journal of Molecular Graphics and Modelling, Volume 41 Since 3D molecular shape is an important determinant of biological activity, designing accurate 3D molecular representations is still of...
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