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Identification of Ligand Templates using Local Structure Alignment for Structure-Based Drug Design

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What this work says

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

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Parallel‐ProBiS: Fast parallel algorithm for local structural comparison of protein structures and binding sites

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Adenine recognition: A motif present in ATP‐, CoA‐, NAD‐, NADP‐, and FAD‐dependent proteins

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Method for comparing the structures of protein ligand‐binding sites and application for predicting protein–drug interactions

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BSP‐SLIM: A blind low‐resolution ligand‐protein docking approach using predicted protein structures

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Protein Structure Comparison by Alignment of Distance Matrices

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Protein Recognition of Adenylate: An Example of a Fuzzy Recognition Template

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Supersites within superfolds. Binding site similarity in the absence of homology 1 1Edited by J. Thornton

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Template-Based Protein Structure Modeling

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A Branch and Bound Algorithm for Matching Protein Structures

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The PDB is a Covering Set of Small Protein Structures

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Recognition of Functional Sites in Protein Structures

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Convergent Evolution of Enzyme Active Sites Is not a Rare Phenomenon

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Protein structure comparison: implications for the nature of ‘fold space’, and structure and function prediction

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Target selection for complex structural genomics

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Progress and challenges in protein structure prediction

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A New Method to Detect Related Function Among Proteins Independent of Sequence and Fold Homology

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Purine nucleoside phosphorylases: properties, functions, and clinical aspects

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Catalytic triads and their relatives

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Pocket Similarity: Are α Carbons Enough?

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PocketAlign A Novel Algorithm for Aligning Binding Sites in Protein Structures

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Identifying and Characterizing Binding Sites and Assessing Druggability

inferredcites →https://doi.org/10.1021/jm0499054openalex-snapshot

CORES: An Automated Method for Generating Three-Dimensional Models of Protein/Ligand Complexes

inferredcites →https://doi.org/10.1021/jm061277yopenalex-snapshot

Diverse, High-Quality Test Set for the Validation of Protein−Ligand Docking Performance

inferredcites →https://doi.org/10.1038/332564a0openalex-snapshot

Dissecting the catalytic triad of a serine protease

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From structure to function: approaches and limitations.

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/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/gki524openalex-snapshot

TM-align: a protein structure alignment algorithm based on the TM-score

inferredcites →https://doi.org/10.1093/nar/gkj062openalex-snapshot

SitesBase: a database for structure-based protein-ligand binding site comparisons

inferredcites →https://doi.org/10.1093/nar/gkq1320openalex-snapshot

ModeRNA: a tool for comparative modeling of RNA 3D structure

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ProBiS-2012: web server and web services for detection of structurally similar binding sites in proteins

inferredcites →https://doi.org/10.1093/protein/11.9.739openalex-snapshot

Protein structure alignment by incremental combinatorial extension (CE) of the optimal path

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A solution for the best rotation to relate two sets of vectors

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Calf spleen purine-nucleoside phosphorylase: crystal structure of the binary complex with a potent multisubstrate analogue inhibitor

inferredcites →https://doi.org/10.1186/1472-6807-6-19openalex-snapshot

LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation.

inferredcites →https://doi.org/10.1371/journal.pcbi.1000405openalex-snapshot

FINDSITELHM: A Threading-Based Approach to Ligand Homology Modeling

inferredcites →https://doi.org/10.1371/journal.pcbi.1000585openalex-snapshot

Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure

What points at this work

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

inferred← citeshttps://doi.org/10.1002/jcc.25813openalex-snapshot

Stalis: A Computational Method for Template‐Based Ab Initio Ligand Design

inferred← citeshttps://doi.org/10.1002/pmic.201900325openalex-snapshot

Profiling the Protein Targets of Unmodified Bio‐Active Molecules with Drug Affinity Responsive Target Stability and Liquid Chromatography/Tandem Mass Spectrometry

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Exhaustive comparison and classification of ligand‐binding surfaces in proteins

inferred← citeshttps://doi.org/10.1002/pro.2890openalex-snapshot

G‐LoSA: An efficient computational tool for local structure‐centric biological studies and drug design

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Adaptive Smith-Waterman residue match seeding for protein structural alignment

inferred← citeshttps://doi.org/10.1002/slct.202404250openalex-snapshot

Molecular Docking and Dynamics Reveal the Potential of Limonene and β ‐Linalool as Natural Fungicides against Mango Anthracnose Pathogen

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G-LoSA for Prediction of Protein-Ligand Binding Sites and Structures

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Binding site comparison for function prediction and pharmaceutical discovery

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PatchSurfers: Two methods for local molecular property-based binding ligand prediction

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Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures

inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00561openalex-snapshot

CHARMM-GUI LBS Finder & Refiner for Ligand Binding Site Prediction and Refinement

inferred← citeshttps://doi.org/10.1021/acs.jcim.1c01156openalex-snapshot

CHARMM-GUI Ligand Designer for Template-Based Virtual Ligand Design in a Binding Site

inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00534openalex-snapshot

ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites

inferred← citeshttps://doi.org/10.1021/acs.jctc.9b00751openalex-snapshot

Ligand-Binding-Site Structure Refinement Using Molecular Dynamics with Restraints Derived from Predicted Binding Site Templates

inferred← citeshttps://doi.org/10.1021/ci4003602openalex-snapshot

Ligand Binding Site Detection by Local Structure Alignment and Its Performance Complementarity

inferred← citeshttps://doi.org/10.1038/s41467-025-63757-9openalex-snapshot

SARST2 high-throughput and resource-efficient protein structure alignment against massive databases

inferred← citeshttps://doi.org/10.1038/s41598-017-10412-zopenalex-snapshot

Global organization of a binding site network gives insight into evolution and structure-function relationships of proteins

inferred← citeshttps://doi.org/10.1093/bioinformatics/btv202openalex-snapshot

GS-align for glycan structure alignment and similarity measurement

inferred← citeshttps://doi.org/10.1093/glycob/cwaa062openalex-snapshot

A systematic analysis of protein–carbohydrate interactions in the Protein Data Bank

inferred← citeshttps://doi.org/10.1093/nar/gku460openalex-snapshot

ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites

inferred← citeshttps://doi.org/10.1111/cbdd.12631openalex-snapshot

Considerations of Protein Subpockets in Fragment‐Based Drug Design

inferred← citeshttps://doi.org/10.1186/s13321-015-0096-0openalex-snapshot

Modeling enzyme-ligand binding in drug discovery

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Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling

inferred← citeshttps://doi.org/10.1371/journal.pone.0190636openalex-snapshot

Genome scale metabolic models as tools for drug design and personalized medicine

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Conservation Pattern, Homology Modeling and Molecular Phylogenetic Study of BMP Ligands

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