标题
Improvements, trends, and new ideas in molecular docking: 2012-2013 in review
作者
关键词
-
出版物
JOURNAL OF MOLECULAR RECOGNITION
Volume 28, Issue 10, Pages 581-604
出版商
Wiley
发表日期
2015-03-25
DOI
10.1002/jmr.2471
参考文献
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- Insights from comprehensive multiple receptor docking to HDAC8
- (2012) Michael Brunsteiner et al. JOURNAL OF MOLECULAR MODELING
- FDA approved drugs complexed to their targets: evaluating pose prediction accuracy of docking protocols
- (2012) Mohammed H. Bohari et al. JOURNAL OF MOLECULAR MODELING
- Exploring Protein Flexibility: Incorporating Structural Ensembles From Crystal Structures and Simulation into Virtual Screening Protocols
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- Understanding the molecular basis of MK2–p38α signaling complex assembly: insights into protein–protein interaction by molecular dynamics and free energy studies
- (2012) Ying Yang et al. Molecular BioSystems
- Lead Hopping forPfDHODH Inhibitors as Antimalarials Based on Pharmacophore Mapping, Molecular Docking and Comparative Binding Energy Analysis (COMBINE): A Three-Layered Virtual Screening Approach
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- FINDSITEX: A Structure-Based, Small Molecule Virtual Screening Approach with Application to All Identified Human GPCRs
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- Quantum.Ligand.Dock: protein-ligand docking with quantum entanglement refinement on a GPU system
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- FTMAP: extended protein mapping with user-selected probe molecules
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- idTarget: a web server for identifying protein targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach
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- Rapid and Accurate Prediction and Scoring of Water Molecules in Protein Binding Sites
- (2012) Gregory A. Ross et al. PLoS One
- Antibody Recognition of Cancer-Related Gangliosides and Their Mimics Investigated Using in silico Site Mapping
- (2012) Mark Agostino et al. PLoS One
- An Efficient Computational Method for Calculating Ligand Binding Affinities
- (2012) Atsushi Suenaga et al. PLoS One
- Can the Energy Gap in the Protein-Ligand Binding Energy Landscape Be Used as a Descriptor in Virtual Ligand Screening?
- (2012) Arsen V. Grigoryan et al. PLoS One
- Using RosettaLigand for Small Molecule Docking into Comparative Models
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- The distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation
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- Do crystal structures obviate the need for theoretical models of GPCRs for structure-based virtual screening?
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- PRL-dock: Protein-ligand docking based on hydrogen bond matching and probabilistic relaxation labeling
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- High performance transcription factor-DNA docking with GPU computing
- (2012) Jiadong Wu et al. Proteome Science
- Fragments to link. A multiple docking strategy for second site binders
- (2012) Márton Vass et al. MedChemComm
- Application of MM-GB/SA and WaterMap to SRC Kinase Inhibitor Potency Prediction
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- Accessible High-Throughput Virtual Screening Molecular Docking Software for Students and Educators
- (2012) Reed B. Jacob et al. PLoS Computational Biology
- FTSite: high accuracy detection of ligand binding sites on unbound protein structures
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- Selective Flexibility of Side-Chain Residues Improves VEGFR-2 Docking Score using AutoDock Vina
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- A GPU-Based Approach to Accelerate Computational Protein-DNA Docking
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- An NMR-based scoring function improves the accuracy of binding pose predictions by docking by two orders of magnitude
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- Hot Spot Analysis for Driving the Development of Hits into Leads in Fragment-Based Drug Discovery
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- Cheminformatics Meets Molecular Mechanics: A Combined Application of Knowledge-Based Pose Scoring and Physical Force Field-Based Hit Scoring Functions Improves the Accuracy of Structure-Based Virtual Screening
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- Integrating Medicinal Chemistry, Organic/Combinatorial Chemistry, and Computational Chemistry for the Discovery of Selective Estrogen Receptor Modulators with Forecaster, a Novel Platform for Drug Discovery
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- Virtual Screening Data Fusion Using Both Structure- and Ligand-Based Methods
- (2011) Fredrik Svensson et al. Journal of Chemical Information and Modeling
- Utilizing Experimental Data for Reducing Ensemble Size in Flexible-Protein Docking
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- Ligand and Decoy Sets for Docking to G Protein-Coupled Receptors
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- Hot Spots and Transient Pockets: Predicting the Determinants of Small-Molecule Binding to a Protein–Protein Interface
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- Virtual screening for compounds that mimic protein-protein interface epitopes
- (2011) Tim Geppert et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Binding affinities in the SAMPL3 trypsin and host–guest blind tests estimated with the MM/PBSA and LIE methods
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- Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function
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- Evaluation of docking performance in a blinded virtual screening of fragment-like trypsin inhibitors
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- Exhaustive search and solvated interaction energy (SIE) for virtual screening and affinity prediction
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- Docking Performance of Fragments and Druglike Compounds
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- A Force Field with Discrete Displaceable Waters and Desolvation Entropy for Hydrated Ligand Docking
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- Enrichment of virtual hits by progressive shape-matching and docking
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- Automatic prediction of flexible regions improves the accuracy of protein-protein docking models
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- The interprotein scoring noises in glide docking scores
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- BSP-SLIM: A blind low-resolution ligand-protein docking approach using predicted protein structures
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- A machine learning approach to predicting protein–ligand binding affinity with applications to molecular docking
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- New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) from Screening Libraries and for Their Exclusion in Bioassays
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- Challenges and advances in computational docking: 2009 in review
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