bioinformatics
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Local functional descriptors for surface comparison based binding prediction

Background:
Molecular recognition in proteins occurs due to appropriate arrangements of physical, chemical, andgeometric properties of an atomic surface. Similar surface regions should create similar bindinginterfaces.
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Automatic design of decision-tree induction algorithms tailored to flexible-receptor docking data

Background This paper addresses the prediction of the free energy of binding of a drug candidate with enzyme InhA associated with Mycobacterium tuberculosis.
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Novel Kinase Inhibitors by Reshuffling Ligand Functionalities Across the Human Kinome

Journal of Chemical Information and ModelingDOI: 10.1021/ci3003842...
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Harvesting Classification Trees for Drug Discovery

Harvesting Classification Trees for Drug Discovery | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci3000216...
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Drug-Target Interaction Prediction by Learning From Local Information and Neighbors

Drug-Target Interaction Prediction by Learning From Local Information and Neighbors | bioinformatics | Scoop.it
Motivation: In silico methods provide efficient ways to predict possible interactions between drugs and targets.
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PolySac3DB: an annotated data base of 3 dimensional structures of polysaccharides

Conclusion:
PolySac3DB is established to maintain information on the detailed 3D structures of polysaccharides.
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Visualising associations between paired `omics' data sets

Three accessible visualization approaches enable meaningful biological hypotheses to be derived from high-throughput "omics" data sets.
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Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target prediction

Background:
Previous studies have noted that drug targets appear to be associated with higher-degree or higher-centrality proteins in interaction networks.
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Are Homology Models Sufficiently Good for Free-Energy Simulations?

Are Homology Models Sufficiently Good for Free-Energy Simulations? | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci300349s...
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USRCAT: real-time ultrafast shape recognition with pharmacophoric constraints

Background:
Ligand-based virtual screening using molecular shape is an important tool for researchers who wish to find novel chemical scaffolds in compound libraries.
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Design of a Three-Dimensional Multitarget Activity Landscape

Design of a Three-Dimensional Multitarget Activity Landscape | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci300444p...
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Recently updated subsets in ZINC

Dear ZINC Fans
We have been updating ZINC. Here are the recent updates:
lead-like, 5.7M, today
shards, 55K, Oct 15
frag-like, 636K, Oct 15
leads-now, 2M, Oct 15
frags-now, 440K, Oct 12
We have also updated many catalogs, too numerous to list here.
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mol2chemfig, a tool for rendering chemical structures from molfile or SMILES format to LATEX code

Displaying chemical structures in LATEX documents currently requires either hand-coding of the structures using one of several LATEX packages, or the inclusion of finished graphics files produced with an external drawing program.
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Deriving how far structural information is transmitted through parallel homodimeric coiled coils: A correlation analysis of helical staggers

Deriving how far structural information is transmitted through parallel homodimeric coiled coils: A correlation analysis of helical staggers | bioinformatics | Scoop.it
Abstract
How local conformation is affected by local sequence is fairly well understood for alpha-helical coiled coils, but less is known about how local conformation is influenced by distant features.
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Structure based function prediction of proteins using fragment library frequency vectors.

Authors: Yadav A, Jayaraman VK
Abstract
The function of the protein is primarily dictated by its structure.
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Current Assessment of Docking into GPCR Crystal Structures and Homology Models: Successes, Challenges, and Guidelines

Current Assessment of Docking into GPCR Crystal Structures and Homology Models: Successes, Challenges, and Guidelines | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci300411b...
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JACOB: A Dynamic Databasefor Computational ChemistryBenchmarking

Journal of Chemical Information and ModelingDOI: 10.1021/ci300374g...
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RMol: A Toolset for Transforming SD/Molfile structure information into R Objects

Background:
The graph-theoretical analysis of molecular networks has a long tradition in chemoinformatics.
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Predicting enzymatic function from global binding site descriptors

Predicting enzymatic function from global binding site descriptors | bioinformatics | Scoop.it
Abstract
Due to the rising number of solved protein structures, computer-based techniques for automatic protein functional annotation and classification into families are of high scientific interest.
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Modeling the Closed and Open State Conformations of the GABAA Ion Channel - Plausible Structural Insights forChannel Gating

Modeling the Closed and Open State Conformations of the GABAA Ion Channel - Plausible Structural Insights forChannel Gating | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci300189a...
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Conformer Generation with OMEGA: Learning from the Data Set and the Analysis of Failures

Conformer Generation with OMEGA: Learning from the Data Set and the Analysis of Failures | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci300314k...
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Structure refinement of protein model decoys requires accurate side-chain placement

Structure refinement of protein model decoys requires accurate side-chain placement | bioinformatics | Scoop.it
Abstract
In this study, the application of temperature-based replica-exchange (T-ReX) simulations for structure refinement of decoys taken from the I-TASSER dataset was examined.
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Dissociation of Membrane-Anchored Heterotrimeric G-Protein Induced by Gα Subunit Binding to GTP

Dissociation of Membrane-Anchored Heterotrimeric G-Protein Induced by Gα Subunit Binding to GTP | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci3003717...
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Update of UCSF DOCK 3.6 on website today

We released a new version of the DOCK 3.6 website. This is the code we use, and the code behind DOCK Blaster. This sub-release (3.6.8) is probably the last in the 3.6 series.
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Sequence recombination improves target specificity in a redesigned collagen peptide abc-type heterotrimer

Sequence recombination improves target specificity in a redesigned collagen peptide abc-type heterotrimer | bioinformatics | Scoop.it
Abstract
Stability of the collagen triple helix is largely governed by its imino acid content, namely the occurrence of proline and 4R-hydroxyproline at the X and Y positions, respectively, of the periodic (Gly-X-Y)n sequence.
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