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Enumeration of 166 Billion Organic Small Molecules in the Chemical Universe Database GDB-17

Enumeration of 166 Billion Organic Small Molecules in the Chemical Universe Database GDB-17 | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci300415d...
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ROSALIND: an addictive bioinformatics learning site | Byte Size Biology

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Shaping a Screening Filefor Maximal Lead DiscoveryEfficiency and Effectiveness: Elimination of Molecular Redundancy

Shaping a Screening Filefor Maximal Lead DiscoveryEfficiency and Effectiveness: Elimination of Molecular Redundancy | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci300372a...
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How Good Are State-of-the-ArtDocking Tools in PredictingLigand Binding Modes in Protein–Protein Interfaces?

How Good Are State-of-the-ArtDocking Tools in PredictingLigand Binding Modes in Protein–Protein Interfaces? | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci3003599...
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Computational protein design suggests that human PCNA-partner interactions are not optimized for affinity

Computational protein design suggests that human PCNA-partner interactions are not optimized for affinity | bioinformatics | Scoop.it
Abstract
Increasing the affinity of binding proteins is invaluable for basic and applied biological research.
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Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach

Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach | bioinformatics | Scoop.it
Motivation: Proteins recognizing short peptide fragments play a central role in cellular signaling.
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Molecular Modeling Tools and Approaches for CFTR and Cystic Fibrosis

Molecular Modeling Tools and Approaches for CFTR and Cystic Fibrosis | bioinformatics | Scoop.it

Cystic fibrosis is a multi-faceted disease resulting from the dysfunction of the CFTR channel. Understanding the structural basis of channel function and the structural origin of the defect is imperative in the development of therapeutic strategies. Here, we describe molecular modeling tools that, in conjunction with complementary experimental tools, lead to significant findings on CFTR channel function and on the effect of the pathogenic mutant F508del.

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Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB

Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB | bioinformatics | Scoop.it
Motivation: Automating the assignment of existing domain and protein family classifications to new sets of sequences is an important task. Current methods often miss assignments because remote relationships fail to achieve statistical significance.
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Efficient a Priori Identificationof Drug ResistantMutations Using Dead-End Elimination and MM-PBSA.

Efficient a Priori Identificationof Drug ResistantMutations Using Dead-End Elimination and MM-PBSA. | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci200626m...
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Protonation States ofthe Catalytic Dyad of β-Secretase(BACE1) in the Presence of Chemically Diverse Inhibitors: A MolecularDocking Study

Protonation States ofthe Catalytic Dyad of β-Secretase(BACE1) in the Presence of Chemically Diverse Inhibitors: A MolecularDocking Study | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci200611t...
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Extracting semantically enriched events frombiomedical literature

Background:
Research into event-based text mining from the biomedical literature has been growing inpopularity to facilitate the development of advanced biomedical text mining systems.
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MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins

Background:
Intrinsically unstructured proteins (IUPs) lack a well-defined three-dimensional structure. Some of them may assume a locally stable structure under specific conditions, e.g.
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The Great Beyond: Biology teachers often dismiss evolution

The Great Beyond: Biology teachers often dismiss evolution | bioinformatics | Scoop.it
That article has a nice quote: “It’s like a math teacher not believing in algebra" http://bit.ly/dI06uy #evolution #biology #education
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admetSAR: A Comprehensive Source and Free Tool for Assessment of Chemical ADMET Properties

admetSAR: A Comprehensive Source and Free Tool for Assessment of Chemical ADMET Properties | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci300367a...
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Open Access Explained. Well. | Byte Size Biology

Open Access Explained. Well. | Byte Size Biology | bioinformatics | Scoop.it
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MP-T: improving membrane protein alignment for structure prediction

MP-T: improving membrane protein alignment for structure prediction | bioinformatics | Scoop.it
Motivation: Membrane proteins are clinically relevant, yet their crystal structures are rare.
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Introducing Drugster: a comprehensive and fully integrated drug design, lead and structure optimization toolkit

Introducing Drugster: a comprehensive and fully integrated drug design, lead and structure optimization toolkit | bioinformatics | Scoop.it
Summary: Drugster is a fully interactive pipeline designed to break the command line barrier and introduce a new user-friendly environment to perform drug design, lead and structure optimization experiments through an efficient combination of the...
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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
We examined the application of temperature-based replica-exchange (T-ReX) simulations for structure refinement of decoys taken from the I-TASSER dataset.
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Exploiting protein flexibility to predict the location of allosteric sites

Background:
Allostery is one of the most powerful and common ways of regulation of protein activity. However,for most allosteric proteins identified to date the mechanistic details of allosteric modulation are notyet well understood.
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Accurate Atom-MappingComputation for BiochemicalReactions

Accurate Atom-MappingComputation for BiochemicalReactions | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci3002217...
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GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data

GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data | bioinformatics | Scoop.it
We present the GFOLD (generalized fold change) algorithm to produce biologically meaningful rankings of differentially expressed genes from RNA-seq data.
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ZINC: A Free Tool to DiscoverChemistry for Biology

ZINC: A Free Tool to DiscoverChemistry for Biology | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci3001277...
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Natural product-likeness score revisited: an open-source,open-data implementation

Background:
Natural product-likeness of a molecule, i.e. similarity of this molecule to the structure space covered by natural products, is a useful criterion in screening compound libraries and in designing new lead compounds.
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Comparison of algorithms for out-of-plane artifacts removal in digital tomosynthesis reconstructions

Abstract: Digital tomosynthesis is a method of limited angle reconstruction of tomographic images produced at variable heights, on the basis of a set of angular projections taken in an arc around human anatomy.
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Bioinformatics Links Directory | Bioinformatics.ca Links Directory

Bioinformatics Links Directory | Bioinformatics.ca Links Directory | bioinformatics | Scoop.it
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