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Ensemble Docking from Homology Models

https://doi.org/10.1021/ct100246y
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Pharmacophores and Pharmacophore Searches
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What do we know and when do we know it?
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Improving database enrichment through ensemble docking
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Recommendations for evaluation of computational methods
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Comparative Modeling of Drug Target Proteins☆
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High-throughput docking as a source of novel drug leads
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Managing protein flexibility in docking and its applications
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Homology modeling in drug discovery: current trends and applications
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Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases
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Flexible ligand docking to multiple receptor conformations: a practical alternative
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Progress and challenges in protein structure prediction
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Comparative Protein Structure Modeling and its Applications to Drug Discovery
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The human proteomics initiative (HPI)
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Reliability of Assessment of Protein Structure Prediction Methods
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Virtual screening and fast automated docking methods
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Structure-based virtual screening: an overview
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High-throughput docking for lead generation
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Identification of a Minimal Subset of Receptor Conformations for Improved Multiple Conformation Docking and Two-Step Scoring
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Screening Drug-Like Compounds by Docking to Homology Models: A Systematic Study
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Evaluating Virtual Screening Methods: Good and Bad Metrics for the “Early Recognition” Problem
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Cross-Docking of Inhibitors into CDK2 Structures. 1
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Scoring Ensembles of Docked Protein:Ligand Interactions for Virtual Lead Optimization
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Molecular Docking Screens Using Comparative Models of Proteins
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Recipes for the Selection of Experimental Protein Conformations for Virtual Screening
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Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments
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Strategic Pooling of Compounds for High-Throughput Screening
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An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics
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Exploring Experimental Sources of Multiple Protein Conformations in Structure-Based Drug Design
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Molecular Properties That Influence the Oral Bioavailability of Drug Candidates
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Kinases, Homology Models, and High Throughput Docking
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Information Decay in Molecular Docking Screens against Holo, Apo, and Modeled Conformations of Enzymes
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Performance of 3D-Database Molecular Docking Studies into Homology Models
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Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
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Unveiling the Full Potential of Flexible Receptor Docking Using Multiple Crystallographic Structures
inferredcites →https://doi.org/10.1021/jm050362nopenalex-snapshot
A Critical Assessment of Docking Programs and Scoring Functions
inferredcites →https://doi.org/10.1021/jm050540copenalex-snapshot
Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects
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Benchmarking Sets for Molecular Docking
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Prediction of Protein−Ligand Interactions. Docking and Scoring: Successes and Gaps
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Target Flexibility: An Emerging Consideration in Drug Discovery and Design
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A review of protein-small molecule docking methods
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A brighter future for protein structure prediction.
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Protein structure modeling for structural genomics.
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Virtual screening of chemical libraries
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Docking and scoring in virtual screening for drug discovery: methods and applications
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Profile hidden Markov models.
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Categorization and characterization of transcript-confirmed constitutively and alternatively spliced introns and exons from human
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CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
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The Protein Data Bank
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The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
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NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
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Pfam: clans, web tools and services
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DrugBank: a knowledgebase for drugs, drug actions and drug targets
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How well can the accuracy of comparative protein structure models be predicted?
inferredcites →https://doi.org/10.1110/ps.062501507openalex-snapshot
Efficient molecular docking of NMR structures: Application to HIV‐1 protease
inferredcites →https://doi.org/10.1126/science.1065659openalex-snapshot
Protein Structure Prediction and Structural Genomics
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The Many Roles of Computation in Drug Discovery
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Comparative Protein Structure Modeling of Genes and Genomes
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Molecular Recognition and Docking Algorithms
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Docking: Successes and Challenges
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Ligand Docking and Structure-based Virtual Screening in Drug Discovery

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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In silico enzyme screening identifies an SDR ketoreductase from Thermus caliditerrae as an attractive biocatalyst and promising candidate for protein engineering
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Structural Insights into the Substrate Transport Mechanisms in GTR Transporters through Ensemble Docking
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Development of an Automatic Pipeline for Participation in the CELPP Challenge
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Comparison of Data Fusion Methods as Consensus Scores for Ensemble Docking
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