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PROLIX: Rapid Mining of Protein–Ligand Interactions in Large Crystal Structure Databases

https://doi.org/10.1021/ci300034x
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What this work says

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

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Protein-Ligand Interactions
inferredcites →https://doi.org/10.1002/prot.10232openalex-snapshot
A new test set for validating predictions of protein–ligand interaction
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A New Method to Detect Related Function Among Proteins Independent of Sequence and Fold Homology
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High-throughput crystallography to enhance drug discovery
inferredcites →https://doi.org/10.1021/ci049733jopenalex-snapshot
An Extensive Test of 14 Scoring Functions Using the PDBbind Refined Set of 800 Protein−Ligand Complexes
inferredcites →https://doi.org/10.1021/ci049870gopenalex-snapshot
Expanded Interaction Fingerprint Method for Analyzing Ligand Binding Modes in Docking and Structure-Based Drug Design
inferredcites →https://doi.org/10.1021/ci050420dopenalex-snapshot
Knowledge-Based Interaction Fingerprint Scoring: A Simple Method for Improving the Effectiveness of Fast Scoring Functions
inferredcites →https://doi.org/10.1021/ci200319eopenalex-snapshot
Rationalizing Tight Ligand Binding through Cooperative Interaction Networks
inferredcites →https://doi.org/10.1021/ci6005257openalex-snapshot
Protein−Protein Binding-Sites Prediction by Protein Surface Structure Conservation
inferredcites →https://doi.org/10.1021/ci8000315openalex-snapshot
Protein Surface Conservation in Binding Sites
inferredcites →https://doi.org/10.1021/ci800322yopenalex-snapshot
Similarity Searching Using Fingerprints of Molecular Fragments Involved in Protein−Ligand Interactions
inferredcites →https://doi.org/10.1021/ci9000053openalex-snapshot
Comparative Assessment of Scoring Functions on a Diverse Test Set
inferredcites →https://doi.org/10.1021/ci900043ropenalex-snapshot
APIF: A New Interaction Fingerprint Based on Atom Pairs and Its Application to Virtual Screening
inferredcites →https://doi.org/10.1021/ci900349yopenalex-snapshot
Alignment-Free Ultra-High-Throughput Comparison of Druggable Protein−Ligand Binding Sites
inferredcites →https://doi.org/10.1021/ci900382eopenalex-snapshot
Combining Machine Learning and Pharmacophore-Based Interaction Fingerprint for in Silico Screening
inferredcites →https://doi.org/10.1021/ci9800211openalex-snapshot
Chemical Similarity Searching
inferredcites →https://doi.org/10.1021/cr960370zopenalex-snapshot
Molecular Recognition of Protein−Ligand Complexes: Applications to Drug Design
inferredcites →https://doi.org/10.1021/jm030331xopenalex-snapshot
Structural Interaction Fingerprint (SIFt): A Novel Method for Analyzing Three-Dimensional Protein−Ligand Binding Interactions
inferredcites →https://doi.org/10.1021/jm030580lopenalex-snapshot
The PDBbind Database: Collection of Binding Affinities for Protein−Ligand Complexes with Known Three-Dimensional Structures
inferredcites →https://doi.org/10.1021/jm048957qopenalex-snapshot
The PDBbind Database: Methodologies and Updates
inferredcites →https://doi.org/10.1021/jm049312topenalex-snapshot
Interaction Profiles of Protein Kinase−Inhibitor Complexes and Their Application to Virtual Screening
inferredcites →https://doi.org/10.1021/jm050381xopenalex-snapshot
Knowledge-Based Design of Target-Focused Libraries Using Protein−Ligand Interaction Constraints
inferredcites →https://doi.org/10.1021/jm9901475openalex-snapshot
High-Throughput Nuclear Magnetic Resonance-Based Screening
inferredcites →https://doi.org/10.1039/b705344dopenalex-snapshot
Design, synthesis and biological evaluation of thrombin inhibitors based on a pyridine scaffold
inferredcites →https://doi.org/10.1073/pnas.0501204102openalex-snapshot
Structural and biochemical basis for selective repression of the orphan nuclear receptor liver receptor homolog 1 by small heterodimer partner
inferredcites →https://doi.org/10.1093/bioinformatics/btq100openalex-snapshot
ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment
inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot
The Protein Data Bank
inferredcites →https://doi.org/10.1093/nar/28.1.304openalex-snapshot
The ENZYME database in 2000
inferredcites →https://doi.org/10.1093/nar/gkg095openalex-snapshot
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
inferredcites →https://doi.org/10.1093/nar/gkh131openalex-snapshot
UniProt: the Universal Protein knowledgebase
inferredcites →https://doi.org/10.1093/nar/gki031openalex-snapshot
Entrez Gene: gene-centered information at NCBI
inferredcites →https://doi.org/10.1093/nar/gki070openalex-snapshot
The Universal Protein Resource (UniProt)
inferredcites →https://doi.org/10.1093/nar/gkl1031openalex-snapshot
Database resources of the National Center for Biotechnology Information
inferredcites →https://doi.org/10.1093/nar/gkn185openalex-snapshot
MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions
inferredcites →https://doi.org/10.1093/nar/gkp405openalex-snapshot
MolLoc: a web tool for the local structural alignment of molecular surfaces
inferredcites →https://doi.org/10.1093/nar/gkq1062openalex-snapshot
IUPHAR-DB: new receptors and tools for easy searching and visualization of pharmacological data
inferredcites →https://doi.org/10.1093/nar/gkr987openalex-snapshot
MEROPS: the database of proteolytic enzymes, their substrates and inhibitors
inferredcites →https://doi.org/10.1111/j.1747-0285.2005.00323.xopenalex-snapshot
Structural Interaction Fingerprints: A New Approach to Organizing, Mining, Analyzing, and Designing Protein–Small Molecule Complexes
inferredcites →https://doi.org/10.1111/j.1747-0285.2008.00762.xopenalex-snapshot
CREDO: A Protein–Ligand Interaction Database for Drug Discovery
inferredcites →https://doi.org/10.1111/j.1747-0285.2009.00829.xopenalex-snapshot
Utilizing Target–Ligand Interaction Information in Fingerprint Searching for Ligands of Related Targets
inferredcites →https://doi.org/10.1111/j.1747-0285.2009.00890.xopenalex-snapshot
Three‐Dimensional Protein–Ligand Interaction Scaling of Two‐Dimensional Fingerprints
inferredcites →https://doi.org/10.1111/j.1747-0285.2010.00993.xopenalex-snapshot
Crystal Structures of IL‐2‐inducible T cell Kinase Complexed with Inhibitors: Insights into Rational Drug Design and Activity Regulation
inferredcites →https://doi.org/10.1186/1741-7007-5-43openalex-snapshot
Spatial chemical conservation of hot spot interactions in protein-protein complexes

What points at this work

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

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Molecular Interaction Fingerprints
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Towards the Next Generation of Computational Chemogenomics Tools
inferred← citeshttps://doi.org/10.1002/wcms.1192openalex-snapshot
Protein–ligand interaction databases: advanced tools to mine activity data and interactions on a structural level
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Integration of Automated Workflow in Chemoinformatics for Drug Discovery
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C-H…pi interactions in proteins: prevalence, pattern of occurrence, residue propensities, location, and contribution to protein stability
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User-centric design of a 3D search interface for protein-ligand complexes
inferred← citeshttps://doi.org/10.1016/bs.apcsb.2014.06.001openalex-snapshot
The Interplay Between Molecular Modeling and Chemoinformatics to Characterize Protein–Ligand and Protein–Protein Interactions Landscapes for Drug Discovery
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From cheminformatics to structure-based design: Web services and desktop applications based on the NAOMI library
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c02173openalex-snapshot
SiteMatcher: A Web Server for Structure-Based Drug Design Using Protein–Ligand Interaction Patterns
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00561openalex-snapshot
Index-Based Searching of Interaction Patterns in Large Collections of Protein–Ligand Interfaces
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.1c01046openalex-snapshot
Searching Geometric Patterns in Protein Binding Sites and Their Application to Data Mining in Protein Kinase Structures
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.5b01756openalex-snapshot
Interactive and Versatile Navigation of Structural Databases
inferred← citeshttps://doi.org/10.1021/ci300523ropenalex-snapshot
Subpocket Analysis Method for Fragment-Based Drug Discovery
inferred← citeshttps://doi.org/10.1021/ci300566nopenalex-snapshot
Encoding Protein–Ligand Interaction Patterns in Fingerprints and Graphs
inferred← citeshttps://doi.org/10.1080/07391102.2021.1873189openalex-snapshot
Molecular elucidation of pancreatic elastase inhibition by baicalein
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa693openalex-snapshot
GeoMine: interactive pattern mining of protein–ligand interfaces in the Protein Data Bank
inferred← citeshttps://doi.org/10.1093/database/bat049openalex-snapshot
CREDO: a structural interactomics database for drug discovery
inferred← citeshttps://doi.org/10.1093/nar/gkab294openalex-snapshot
PLIP 2021: expanding the scope of the protein–ligand interaction profiler to DNA and RNA
inferred← citeshttps://doi.org/10.1093/nar/gkv315openalex-snapshot
PLIP: fully automated protein–ligand interaction profiler
inferred← citeshttps://doi.org/10.1101/2022.02.09.479729openalex-snapshot
Identification of Catechins Binding Pockets in Monomeric A β 42 Through Ensemble Docking and MD Simulations
inferred← citeshttps://doi.org/10.1109/tcbb.2019.2892099openalex-snapshot
nAPOLI: A Graph-Based Strategy to Detect and Visualize Conserved Protein-Ligand Interactions in Large-Scale
inferred← citeshttps://doi.org/10.1111/cbdd.12631openalex-snapshot
Considerations of Protein Subpockets in Fragment‐Based Drug Design
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fingeRNAt—A novel tool for high-throughput analysis of nucleic acid-ligand interactions
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Identification of Catechins’ Binding Sites in Monomeric Aβ42 through Ensemble Docking and MD Simulations
inferred← citeshttps://doi.org/10.3390/molecules26154625openalex-snapshot
MolADI: A Web Server for Automatic Analysis of Protein–Small Molecule Dynamic Interactions
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