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Three-Dimensional Structure Database of Natural Metabolites
(3DMET): A Novel Database of Curated 3D Structures

Three-Dimensional Structure Database of Natural Metabolites<br/>(3DMET): A Novel Database of Curated 3D Structures | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci300309k
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GenePainter: a fast tool for aligning gene structures of eukaryotic protein families, visualizing the alignments and mapping gene structures onto protein structures

Background:
All sequenced eukaryotic genomes have been shown to possess at least a few introns. This includes those unicellular organisms, which were previously suspected to be intron-less.
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MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships

MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships | bioinformatics | Scoop.it
Summary: MODexplorer is an integrated tool aimed at exploring the sequence, structural and functional diversity in protein families useful in homology modeling and in analyzing protein families in general.
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Predicting protein {beta}-sheet contacts using a maximum entropy-based correlated mutation measure

Predicting protein {beta}-sheet contacts using a maximum entropy-based correlated mutation measure | bioinformatics | Scoop.it
Motivation: The problem of ab initio protein folding is one of the most difficult in modern computational biology. The prediction of residue contacts within a protein provides a more tractable immediate step.
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BioSM: Metabolomics Tool for Identifying Endogenous
Mammalian Biochemical Structures in Chemical Structure Space

BioSM: Metabolomics Tool for Identifying Endogenous<br/>Mammalian Biochemical Structures in Chemical Structure Space | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci300512q
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Strategy to Target the Substrate Binding site of SET
Domain Protein Methyltransferases

Strategy to Target the Substrate Binding site of SET<br/>Domain Protein Methyltransferases | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci300596x
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GalaxyGemini: a web server for protein homo-oligomer structure prediction based on similarity

GalaxyGemini: a web server for protein homo-oligomer structure prediction based on similarity | bioinformatics | Scoop.it
Summary: A large number of proteins function as homooligomers; therefore, predicting homo-oligomeric structure of proteins is of primary importance for understanding protein function at the molecular level.
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As good as it gets? Folding molecular dynamics simulations of the LytA choline-binding peptide result to an exceptionally accurate model of the peptide structure

As good as it gets? Folding molecular dynamics simulations of the LytA choline-binding peptide result to an exceptionally accurate model of the peptide structure | bioinformatics | Scoop.it
Available online 16 February 2013 Publication year: 2013 Source:Journal of Molecular Graphics and Modelling Folding simulations of a choline-binding peptide derived from the Streptococcus pneumoniae LytA protein converged to a model...
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The prediction of palmitoylation site locations using a multiple feature extraction method

The prediction of palmitoylation site locations using a multiple feature extraction method | bioinformatics | Scoop.it
March 2013 Publication year: 2013 Source:Journal of Molecular Graphics and Modelling, Volume 40 As an extremely important and ubiquitous post-translational lipid modification, palmitoylation plays a significant role in a variety of...
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Consensus Docking: Improving
the Reliability of Docking
in a Virtual Screening Context

Consensus Docking: Improving<br/>the Reliability of Docking<br/>in a Virtual Screening Context | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci300399w
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Graph-Based Consensus Clustering for Combining Multiple Clusterings of Chemical Structures

Graph-Based Consensus Clustering for Combining Multiple Clusterings of Chemical Structures | bioinformatics | Scoop.it
Abstract
Consensus clustering methods have been successfully used for combining multiple classifiers in many areas such as machine learning, applied statistics, pattern recognition and bioinformatics.
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SwarmDock: a server for flexible protein-protein docking

SwarmDock: a server for flexible protein-protein docking | bioinformatics | Scoop.it
Summary: Protein-protein interactions are central to almost all biological functions, and the atomic details of such interactions can yield insights into the mechanisms which underlie these functions.
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How Do Metabolites Differ
from Their Parent Molecules
and How Are They Excreted?

How Do Metabolites Differ<br/>from Their Parent Molecules<br/>and How Are They Excreted? | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci300487z
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git can facilitate greater reproducibility and increased transparency in science

Background Reproducibility is the hallmark of good science.Maintaining a high degree of transparency in scientific reporting isessential not just for gaining trust and credibility within thescientific community but also for facilitating the...
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iBIOMES: Managing and Sharing Biomolecular Simulation
Data in a Distributed Environment

iBIOMES: Managing and Sharing Biomolecular Simulation<br/>Data in a Distributed Environment | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci300524j
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Pharmacophore modeling, virtual screening, docking and in silico ADMET analysis of protein kinase B (PKB β) inhibitors

Pharmacophore modeling, virtual screening, docking and in silico ADMET analysis of protein kinase B (PKB β) inhibitors | bioinformatics | Scoop.it
Available online 24 February 2013
Publication year: 2013
Source:Journal of Molecular Graphics and Modelling

Protein kinase B (PKB) is a key mediator of proliferation and survival pathways that are critical for cancer growth.
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SVM Based Descriptor Selection and Classification of Neurodegenerative Disease Drugs for Pharmacological Modeling

SVM Based Descriptor Selection and Classification of Neurodegenerative Disease Drugs for Pharmacological Modeling | bioinformatics | Scoop.it
Abstract
Systems pharmacological modeling of drug mode of action for the next generation of multitarget drugs may open new routes for drug design and discovery.
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Mixed Monte Carlo/Molecular Dynamics Simulations of the Prion Protein

Mixed Monte Carlo/Molecular Dynamics Simulations of the Prion Protein | bioinformatics | Scoop.it
Available online 26 February 2013 Publication year: 2013 Source:Journal of Molecular Graphics and Modelling In this paper we present the results of mixed Monte Carlo/Molecular Dynamics simulations (MC/MD) of the D178N mutant of the...
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Predicting Potent Compounds
via Model-Based Global Optimization

Predicting Potent Compounds<br/>via Model-Based Global Optimization | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci3004682
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Prediction of Ligand-Induced
Structural Polymorphism
of Receptor Interaction Sites Using Machine Learning

Prediction of Ligand-Induced<br/>Structural Polymorphism<br/>of Receptor Interaction Sites Using Machine Learning | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci300458g
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A two-step drug repositioning method based on a protein-protein interaction network of genes shared by two diseases and the similarity of drugs.

Authors: Fukuoka Y, Takei D, Ogawa H
Abstract
The present study proposed a two-step drug repositioning method based on a protein-protein interaction (PPI) network of two diseases and the similarity of the drugs prescribed for one of the two.
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Chemogenomics Approaches
to Rationalizing the Mode-of-Action
of Traditional Chinese and Ayurvedic Medicines

Chemogenomics Approaches<br/>to Rationalizing the Mode-of-Action<br/>of Traditional Chinese and Ayurvedic Medicines | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci3005513
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Fast Protein Binding Site
Comparison via an Index-Based Screening Technology

Fast Protein Binding Site<br/>Comparison via an Index-Based Screening Technology | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci300469h
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Predicting PDZ domain mediated protein interactions from structure

Background: PDZ domains are structural protein domains that recognize simple linear amino acid motifs, often at protein C-termini, and mediate protein-protein interactions (PPIs) in important biological processes, such as ion channel regulation,...
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Simultaneous prediction of protein secondary structure and trans-membrane spans

Simultaneous prediction of protein secondary structure and trans-membrane spans | bioinformatics | Scoop.it
Abstract
Prediction of trans-membrane spans and secondary structure from the protein sequence is generally the first step in the structural characterization of (membrane) proteins.
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