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Consensus Methods for Combining Multiple Clusterings
of Chemical Structures

Consensus Methods for Combining Multiple Clusterings<br/>of Chemical Structures | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci300442u
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Consensus Methods for Combining Multiple Clusterings
of Chemical Structures

Consensus Methods for Combining Multiple Clusterings<br/>of Chemical Structures | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci300442u
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Characterizing Binding of Small Molecules. II. Evaluating
the Potency of Small Molecules to Combat Resistance Based on Docking
Structures

Characterizing Binding of Small Molecules. II. Evaluating<br/>the Potency of Small Molecules to Combat Resistance Based on Docking<br/>Structures | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci400011c
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Ranking multiple docking solutions based on the conservation of inter-residue contacts

Ranking multiple docking solutions based on the conservation of inter-residue contacts | bioinformatics | Scoop.it
Abstract
Molecular docking is the method of choice for investigating the molecular basis of recognition in a large number of functional protein complexes.
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In Silico Fragment-Based Drug Discovery: Setup and
Validation of a Fragment-to-Lead Computational Protocol Using S4MPLE

Journal of Chemical Information and ModelingDOI: 10.1021/ci4000163
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Insight into structural and Biochemical determinants of substrate specificity of PFI1625c: Correlation analysis of protein-peptide molecular models

Insight into structural and Biochemical determinants of substrate specificity of PFI1625c: Correlation analysis of protein-peptide molecular models | bioinformatics | Scoop.it
Available online 8 April 2013
Publication year: 2013
Source:Journal of Molecular Graphics and Modelling

Bioinformatics and sequence comparison indicate PFI1625c as a putative metalloprotease present in plasmodium genome.
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Adverse Drug Events: Database Construction and in
Silico Prediction

Adverse Drug Events: Database Construction and in<br/>Silico Prediction | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci4000079
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Structure-Based Virtual Screening of MT2 Melatonin Receptor: Influence of Template Choice and Structural
Refinement

Structure-Based Virtual Screening of MT2 Melatonin Receptor: Influence of Template Choice and Structural<br/>Refinement | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci4000147
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Network predicting drug's anatomical therapeutic chemical code

Network predicting drug's anatomical therapeutic chemical code | bioinformatics | Scoop.it
Motivation: Discovering drug's Anatomical Therapeutic Chemical (ATC) classification rules at molecular level is of vital importance to understand a vast majority of drugs action.
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Automated Docking with Protein Flexibility in the
Design of Femtomolar “Click Chemistry” Inhibitors of
Acetylcholinesterase

Automated Docking with Protein Flexibility in the<br/>Design of Femtomolar “Click Chemistry” Inhibitors of<br/>Acetylcholinesterase | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci300545a
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Priorities for improving drug research, development and regulation

Nature Reviews Drug Discovery 12, 247 (2013).
doi:10.1038/nrd3981
Authors: Susan R.
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The use of soluble protein structures in modeling helical proteins in a layered membrane

The use of soluble protein structures in modeling helical proteins in a layered membrane | bioinformatics | Scoop.it
Journal of Biomolecular Structure and Dynamics, Volume 0, Issue 0, Page 1-11, Ahead of Print.
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GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit | bioinformatics | Scoop.it
Motivation: Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many...
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Enrichment Factor Analyses on G-Protein Coupled
Receptors with Known Crystal Structure

Enrichment Factor Analyses on G-Protein Coupled<br/>Receptors with Known Crystal Structure | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci4000745
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Use of Experimental Design To Optimize Docking Performance:
The Case of LiGenDock, the Docking Module of Ligen, a New De Novo
Design Program

Use of Experimental Design To Optimize Docking Performance:<br/>The Case of LiGenDock, the Docking Module of Ligen, a New De Novo<br/>Design Program | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci400079k
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Analyzing the effect of homogeneous frustration in protein folding

Analyzing the effect of homogeneous frustration in protein folding | bioinformatics | Scoop.it
Abstract
The energy landscape theory has been an invaluable theoretical framework in the understanding of biological processes such as protein folding, oligomerization and functional transitions.
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Development of the Knowledge-Based and Empirical Combined
Scoring Algorithm (KECSA) To Score Protein–Ligand Interactions

Journal of Chemical Information and ModelingDOI: 10.1021/ci300619x
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Prediction
of Compounds with Closely Related Activity
Profiles Using Weighted Support Vector Machine Linear Combinations

Prediction<br/>of Compounds with Closely Related Activity<br/>Profiles Using Weighted Support Vector Machine Linear Combinations | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci400090t
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An Extensive and Diverse Set of Molecular Overlays
for the Validation of Pharmacophore Programs

An Extensive and Diverse Set of Molecular Overlays<br/>for the Validation of Pharmacophore Programs | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci400020a
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Prediction of Polypharmacological Profiles of Drugs
by the Integration of Chemical, Side Effect, and Therapeutic Space

Prediction of Polypharmacological Profiles of Drugs<br/>by the Integration of Chemical, Side Effect, and Therapeutic Space | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci400010x
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The influence of the inactives subset generation on the performance of machine learning methods

Background:
A growing popularity of machine learning methods application in virtual screening, in both classification and regression tasks, can be observed in the past few years.
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Time-Split
Cross-Validation as a Method for Estimating
the Goodness of Prospective Prediction.

Time-Split<br/>Cross-Validation as a Method for Estimating<br/>the Goodness of Prospective Prediction. | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci400084k
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Feasibility of Using Molecular Docking-Based Virtual
Screening for Searching Dual Target Kinase Inhibitors

Feasibility of Using Molecular Docking-Based Virtual<br/>Screening for Searching Dual Target Kinase Inhibitors | bioinformatics | Scoop.it
Journal of Chemical Information and ModelingDOI: 10.1021/ci400065e
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Probing the structure of Mycobacterium tuberculosis MbtA: model validation using molecular dynamics simulations and docking studies

Probing the structure of Mycobacterium tuberculosis MbtA: model validation using molecular dynamics simulations and docking studies | bioinformatics | Scoop.it
Journal of Biomolecular Structure and Dynamics, Volume 0, Issue 0, Page 1-16, Ahead of Print.
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A benchmark server using high resolution protein structure data, and benchmark results for membrane helix predictions

Background:
Helical membrane proteins are vital for the interaction of cells with their environment.
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Graphical ZINC browser available

Dear ZINC Fans
Prof. Jean-Louis Reymond and his student Mahendra Awale have generously arranged for an MQN browser of ZINC. A preliminary version of the "all purchasable" subset is now available.
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