rDock: a fast, versatile and open source program for docking ligands to proteins and nucleic acids - Wikidata - awgldk - TriplyDB

rDock: a fast, versatile and open source program for docking ligands to proteins and nucleic acids

rDock: a fast, versatile and open source program for docking ligands to proteins and nucleic acids

http://www.wikidata.org/entity/Q28537716

about

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics Charting a Path to Success in Virtual Screening Small molecule compounds targeting miRNAs for cancer therapy Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets Open source molecular modeling Building a virtual ligand screening pipeline using free software: a survey SPA-LN: a scoring function of ligand-nucleic acid interactions via optimizing both specificity and affinity.Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules.DockBench: An Integrated Informatic Platform Bridging the Gap between the Robust Validation of Docking Protocols and Virtual Screening Simulations.NRGsuite: a PyMOL plugin to perform docking simulations in real time using FlexAID Unveiling a novel transient druggable pocket in BACE-1 through molecular simulations: Conformational analysis and binding mode of multisite inhibitors.DARC: Mapping Surface Topography by Ray-Casting for Effective Virtual Screening at Protein Interaction Sites.Fragment oriented molecular shapes Combining self- and cross-docking as benchmark tools: the performance of DockBench in the D3R Grand Challenge 2.Aromatic interactions at the ligand-protein interface: Implications for the development of docking scoring functions.Pharmacological tools based on imidazole scaffold proved the utility of PDE10A inhibitors for Parkinson's disease.Octopus: a platform for the virtual high-throughput screening of a pool of compounds against a set of molecular targets.Software for molecular docking: a review.Docking-undocking combination applied to the D3R Grand Challenge 2015.Docking small peptides remains a great challenge: an assessment using AutoDock Vina.Fragment-Based Analysis of Ligand Dockings Improves Classification of Actives.Molecular Rationale behind the Differential Substrate Specificity of Bacterial RND Multi-Drug Transporters.AMMOS2: a web server for protein-ligand-water complexes refinement via molecular mechanics Attracting cavities for docking. Replacing the rough energy landscape of the protein by a smooth attracting landscape.Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach.Machine Learning Consensus Scoring Improves Performance Across Targets in Structure-Based Virtual Screening.A Database of Force-Field Parameters, Dynamics, and Properties of Antimicrobial Compounds.Molecular Modeling of Multidrug Properties of Resistance Nodulation Division (RND) Transporters.Dimerization: a structural feature for the protection of hepatitis E virus capsid protein against trypsinization.Identification of potential isoform-selective histone deacetylase inhibitors for cancer therapy: a combined approach of structure-based virtual screening, ADMET prediction and molecular dynamics simulation assay.Effects of the Protonation State of Titratable Residues and the Presence of Water Molecules on Nocodazole Binding to β-Tubulin.In silico design and bioevaluation of selective benzotriazepine BRD4 inhibitors with potent antiosteoclastogenic activity.Dynamic undocking and the quasi-bound state as tools for drug discovery.DockBench as docking selector tool: the lesson learned from D3R Grand Challenge 2015.Comparative assessment of strategies to identify similar ligand-binding pockets in proteins.Reliability analysis and optimization of the consensus docking approach for the development of virtual screening studies.Chemical Space Expansion of Bromodomain Ligands Guided by in Silico Virtual Couplings (AutoCouple).Molecular Determinants of the Promiscuity of MexB and MexY Multidrug Transporters of Pseudomonas aeruginosa.eModel-BDB: a database of comparative structure models of drug-target interactions from the Binding Database Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview

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rDock: a fast, versatile and open source program for docking ligands to proteins and nucleic acids

http://www.wikidata.org/entity/Q28537716

description

2014 nî lūn-bûn

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2014 թուականի Ապրիլին հրատարակուած գիտական յօդուած

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2014 թվականի ապրիլին հրատարակված գիտական հոդված

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2014年の論文

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2014年論文

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2014年論文

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2014年論文

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2014年論文

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2014年論文

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2014年论文

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name

rDock: a fast, versatile and o ...... to proteins and nucleic acids

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rDock: a fast, versatile and o ...... to proteins and nucleic acids

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rDock: a fast, versatile and o ...... to proteins and nucleic acids

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rDock: a fast, versatile and o ...... to proteins and nucleic acids

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JOURNAL.PCBI.1003571

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PLOS Computational Biology

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rDock: a fast, versatile and o ...... to proteins and nucleic acids

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A Beatriz Garmendia-Doval

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Daniel Alvarez-Garcia

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Peter Schmidtke

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Roderick E Hubbard

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S David Morley

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Szilveszter Juhos

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P2860

Open Babel: An open chemical toolbox

DOCK 6: combining techniques to model RNA-small molecule complexes

Structure-based virtual screening for drug discovery: a problem-centric review

Discovery of a potent CDK2 inhibitor with a novel binding mode, using virtual screening and initial, structure-guided lead scoping

Novel adenosine-derived inhibitors of 70 kDa heat shock protein, discovered through structure-based design

ZINC--a free database of commercially available compounds for virtual screening

Combining hit identification strategies: fragment-based and in silico approaches to orally active 2-aminothieno[2,3-d]pyrimidine inhibitors of the Hsp90 molecular chaperone

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy

Benchmarking sets for molecular docking

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e1003571

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scholarly article

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2021291

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10.1371/JOURNAL.PCBI.1003571

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4

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10

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Sergio Ruiz-Carmona

Nicolas Foloppe

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2014-04-01T00:00:00Z

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261603906

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24722481

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open-source software

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3983074

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