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FINDSITE comb : A Threading/Structure-Based, Proteomic-Scale Virtual Ligand Screening Approach
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Outgoing claims: the papers this work cites, builds on, or argues with.
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Flexible protein–ligand docking by global energy optimization in internal coordinates
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Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking
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Q‐Dock: Low‐resolution flexible ligand docking with pocket‐specific threading restraints
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AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
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Q‐DockLHM: Low‐resolution refinement for ligand comparative modeling
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ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
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Pharmacophore‐based molecular docking to account for ligand flexibility
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Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm
inferredcites →https://doi.org/10.1002/prot.20264openalex-snapshot
Scoring function for automated assessment of protein structure template quality
inferredcites →https://doi.org/10.1002/prot.20308openalex-snapshot
Fold recognition by combining sequence profiles derived from evolution and from depth‐dependent structural alignment of fragments
inferredcites →https://doi.org/10.1002/prot.22566openalex-snapshot
Comparison of structure‐based and threading‐based approaches to protein functional annotation
inferredcites →https://doi.org/10.1002/prot.23165openalex-snapshot
BSP‐SLIM: A blind low‐resolution ligand‐protein docking approach using predicted protein structures
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Template‐based protein structure modeling using TASSERVMT
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Approaches to Measure Chemical Similarity – a Review
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Similarity Metrics and Descriptor Spaces – Which Combinations to Choose?
inferredcites →https://doi.org/10.1007/s10822-007-9114-2openalex-snapshot
Surflex-Dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search
inferredcites →https://doi.org/10.1007/s10822-012-9565-yopenalex-snapshot
Evaluation of DOCK 6 as a pose generation and database enrichment tool
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Recognizing Protein-Ligand Binding Sites by Global Structural Alignment and Local Geometry Refinement
inferredcites →https://doi.org/10.1016/s0022-2836(77)80200-3openalex-snapshot
The protein data bank: A computer-based archival file for macromolecular structures
inferredcites →https://doi.org/10.1016/s0167-7799(01)01696-1openalex-snapshot
Industrial-scale, genomics-based drug design and discovery
inferredcites →https://doi.org/10.1021/ci049714+openalex-snapshot
ZINC − A Free Database of Commercially Available Compounds for Virtual Screening
inferredcites →https://doi.org/10.1021/ci100235nopenalex-snapshot
Comprehensive Structural and Functional Characterization of the Human Kinome by Protein Structure Modeling and Ligand Virtual Screening
inferredcites →https://doi.org/10.1021/ci900056copenalex-snapshot
Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy
inferredcites →https://doi.org/10.1021/ci970437zopenalex-snapshot
On the Properties of Bit String-Based Measures of Chemical Similarity
inferredcites →https://doi.org/10.1021/jm020406hopenalex-snapshot
Surflex: Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-Based Search Engine
inferredcites →https://doi.org/10.1021/jm0306430openalex-snapshot
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
inferredcites →https://doi.org/10.1021/jm030644sopenalex-snapshot
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening
inferredcites →https://doi.org/10.1021/jm050040jopenalex-snapshot
Parameter Estimation for Scoring Protein−Ligand Interactions Using Negative Training Data
inferredcites →https://doi.org/10.1021/jm0608356openalex-snapshot
Benchmarking Sets for Molecular Docking
inferredcites →https://doi.org/10.1021/jp211052jopenalex-snapshot
Further Evidence for the Likely Completeness of the Library of Solved Single Domain Protein Structures
inferredcites →https://doi.org/10.1021/mp1002976openalex-snapshot
Cross-Reactivity Virtual Profiling of the Human Kinome by X-ReactKIN: A Chemical Systems Biology Approach
inferredcites →https://doi.org/10.1021/mp3000716openalex-snapshot
FINDSITEX: A Structure-Based, Small Molecule Virtual Screening Approach with Application to All Identified Human GPCRs
inferredcites →https://doi.org/10.1023/a:1011115820450openalex-snapshot
DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
inferredcites →https://doi.org/10.1038/nrd3368openalex-snapshot
Impact of high-throughput screening in biomedical research
inferredcites →https://doi.org/10.1073/pnas.0305695101openalex-snapshot
Automated structure prediction of weakly homologous proteins on a genomic scale
inferredcites →https://doi.org/10.1073/pnas.0707684105openalex-snapshot
A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
inferredcites →https://doi.org/10.1073/pnas.89.22.10915openalex-snapshot
Amino acid substitution matrices from protein blocks.
inferredcites →https://doi.org/10.1093/nar/gki524openalex-snapshot
TM-align: a protein structure alignment algorithm based on the TM-score
inferredcites →https://doi.org/10.1093/nar/gkj067openalex-snapshot
DrugBank: a comprehensive resource for in silico drug discovery and exploration
inferredcites →https://doi.org/10.1093/nar/gkm948openalex-snapshot
GLIDA: GPCR ligand database for chemical genomics drug discovery database and tools update
inferredcites →https://doi.org/10.1093/nar/gkq406openalex-snapshot
3DLigandSite: predicting ligand-binding sites using similar structures
inferredcites →https://doi.org/10.1093/nar/gkr777openalex-snapshot
ChEMBL: a large-scale bioactivity database for drug discovery
inferredcites →https://doi.org/10.1093/nar/gks372openalex-snapshot
COFACTOR: an accurate comparative algorithm for structure-based protein function annotation
inferredcites →https://doi.org/10.1186/1471-2105-9-531openalex-snapshot
Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score
inferredcites →https://doi.org/10.1201/9781420028775.ch13openalex-snapshot
Pharmacophore-Based Molecular Docking
inferredcites →https://doi.org/10.1371/journal.pcbi.1000405openalex-snapshot
FINDSITELHM: A Threading-Based Approach to Ligand Homology Modeling
inferredcites →https://doi.org/10.2174/138920307781369382openalex-snapshot
Structure-Based Drug Design: Docking and Scoring
inferredcites →https://doi.org/10.2174/138920307781369427openalex-snapshot
Virtual Screening in Drug Discovery - A Computational Perspective
inferredcites →https://doi.org/10.3791/3259openalex-snapshot
A Protocol for Computer-Based Protein Structure and Function Prediction
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Virtual Screening and Bioactivity Modeling for G Protein‐Coupled Receptors
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Computational Studies of Smell and Taste Receptors
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SPOT‐Ligand: Fast and effective structure‐based virtual screening by binding homology search according to ligand and receptor similarity
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Chemical space of Escherichia coli dihydrofolate reductase inhibitors: New approaches for discovering novel drugs for old bugs
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FRAGSITE2 : A structure and fragment‐based approach for virtual ligand screening
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In silico methods for drug repurposing and pharmacology
inferred← citeshttps://doi.org/10.1007/978-1-0716-1787-8_13openalex-snapshot
Ultrahigh Throughput Protein–Ligand Docking with Deep Learning
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Repurposed FDA-approved drugs targeting genes influencing aging can extend lifespan and healthspan in rotifers
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Computational methods and tools for binding site recognition between proteins and small molecules: from classical geometrical approaches to modern machine learning strategies
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Targeting WEE1 kinase: an integrated machine learning–cheminformatics framework for ultra-large-scale virtual screening and novel inhibitor discovery
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Molecular docking-based computational platform for high-throughput virtual screening
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On the Use of Knowledge-Based Potentials for the Evaluation of Models of Protein–Protein, Protein–DNA, and Protein–RNA Interactions
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In Silico Databases and Tools for Drug Repurposing
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Principles of computational drug designing and drug repurposing—An algorithmic approach
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Novel small molecule binders of human N-glycanase 1, a key player in the endoplasmic reticulum associated degradation pathway
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Implications of the small number of distinct ligand binding pockets in proteins for drug discovery, evolution and biochemical function
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Pocket detection and interaction-weighted ligand-similarity search yields novel high-affinity binders for Myocilin-OLF, a protein implicated in glaucoma
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ClusPro LigTBM: Automated Template-based Small Molecule Docking
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Are predicted protein structures of any value for binding site prediction and virtual ligand screening?
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Template-based prediction of protein function
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Insights into Disease-Associated Mutations in the Human Proteome through Protein Structural Analysis
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Ranking Enzyme Structures in the PDB by Bound Ligand Similarity to Biological Substrates
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Improving drug safety: From adverse drug reaction knowledge discovery to clinical implementation
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FRAGSITE: A Fragment-Based Approach for Virtual Ligand Screening
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EViS: An Enhanced Virtual Screening Approach Based on Pocket–Ligand Similarity
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PoLi : A Virtual Screening Pipeline Based on Template Pocket and Ligand Similarity
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00309openalex-snapshot
FINDSITEcomb2.0: A New Approach for Virtual Ligand Screening of Proteins and Virtual Target Screening of Biomolecules
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SPOT-Peptide: Template-Based Prediction of Peptide-Binding Proteins and Peptide-Binding Sites
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Implications of the Essential Role of Small Molecule Ligand Binding Pockets in Protein–Protein Interactions
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Utility of the Morgan Fingerprint in Structure-Based Virtual Ligand Screening
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Why Is There a Glass Ceiling for Threading Based Protein Structure Prediction Methods?
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MEDICASCY: A Machine Learning Approach for Predicting Small-Molecule Drug Side Effects, Indications, Efficacy, and Modes of Action
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An Unbiased Method To Build Benchmarking Sets for Ligand-Based Virtual Screening and its Application To GPCRs
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Comprehensive prediction of drug-protein interactions and side effects for the human proteome
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