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

https://doi.org/10.1002/pro.2890
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What this work says

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

inferredcites →https://doi.org/10.1002/prot.10556openalex-snapshot
Critical assessment of methods of protein structure prediction (CASP)-round V
inferredcites →https://doi.org/10.1002/prot.23165openalex-snapshot
BSP‐SLIM: A blind low‐resolution ligand‐protein docking approach using predicted protein structures
inferredcites →https://doi.org/10.1006/jmbi.1993.1489openalex-snapshot
Protein Structure Comparison by Alignment of Distance Matrices
inferredcites →https://doi.org/10.1006/jmbi.1998.1844openalex-snapshot
Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution
inferredcites →https://doi.org/10.1007/978-3-540-30219-3_17openalex-snapshot
Protein-Protein Interfaces: Recognition of Similar Spatial and Chemical Organizations
inferredcites →https://doi.org/10.1007/bf02022037openalex-snapshot
The shortest augmenting path method for solving assignment problems — Motivation and computational experience
inferredcites →https://doi.org/10.1007/s00018-007-7211-yopenalex-snapshot
Computational protein function prediction: Are we making progress?
inferredcites →https://doi.org/10.1016/0958-1669(91)90084-iopenalex-snapshot
Metal-binding sites in proteins
inferredcites →https://doi.org/10.1016/j.jmb.2004.04.012openalex-snapshot
Recognition of Functional Sites in Protein Structures
inferredcites →https://doi.org/10.1021/bi982362dopenalex-snapshot
Structural Features of Protein−Nucleic Acid Recognition Sites
inferredcites →https://doi.org/10.1021/ci2005687openalex-snapshot
ProBiS-Database: Precalculated Binding Site Similarities and Local Pairwise Alignments of PDB Structures
inferredcites →https://doi.org/10.1021/ci300178eopenalex-snapshot
Identification of Ligand Templates using Local Structure Alignment for Structure-Based Drug Design
inferredcites →https://doi.org/10.1021/ci4003602openalex-snapshot
Ligand Binding Site Detection by Local Structure Alignment and Its Performance Complementarity
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/nrm3838openalex-snapshot
Regulation of microRNA biogenesis
inferredcites →https://doi.org/10.1073/pnas.87.15.5648openalex-snapshot
Where metal ions bind in proteins.
inferredcites →https://doi.org/10.1073/pnas.89.22.10915openalex-snapshot
Amino acid substitution matrices from protein blocks.
inferredcites →https://doi.org/10.1074/jbc.m112.361295openalex-snapshot
Structural Basis for Small G Protein Effector Interaction of Ras-related Protein 1 (Rap1) and Adaptor Protein Krev Interaction Trapped 1 (KRIT1)
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/bioinformatics/btq404openalex-snapshot
iAlign: a method for the structural comparison of protein–protein interfaces
inferredcites →https://doi.org/10.1093/bioinformatics/btt024openalex-snapshot
APoc: large-scale identification of similar protein pockets
inferredcites →https://doi.org/10.1093/emboj/cdg359openalex-snapshot
Diversity of protein–protein interactions
inferredcites →https://doi.org/10.1093/nar/gkh039openalex-snapshot
SCOP database in 2004: refinements integrate structure and sequence family data
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/gkl959openalex-snapshot
The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution
inferredcites →https://doi.org/10.1093/nar/gkq1021openalex-snapshot
The RCSB Protein Data Bank: redesigned web site and web services
inferredcites →https://doi.org/10.1093/protein/11.9.739openalex-snapshot
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
inferredcites →https://doi.org/10.1098/rstb.2005.1800openalex-snapshot
Structural biology and bioinformatics in drug design: opportunities and challenges for target identification and lead discovery
inferredcites →https://doi.org/10.1146/annurev-biochem-060408-091030openalex-snapshot
Origins of Specificity in Protein-DNA Recognition
inferredcites →https://doi.org/10.1186/s12859-015-0471-xopenalex-snapshot
PCalign: a method to quantify physicochemical similarity of protein-protein interfaces

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/10.1007/978-1-4939-7015-5_8openalex-snapshot
G-LoSA for Prediction of Protein-Ligand Binding Sites and Structures
inferred← citeshttps://doi.org/10.1007/978-3-031-81728-1_27openalex-snapshot
Molecular Dynamics in Predicting the Stability of Drug-Receptor Interactions
inferred← citeshttps://doi.org/10.1016/b978-0-323-95502-7.00202-5openalex-snapshot
Finding Second-Generation Pharmacochaperones: Getting Help From Computational Methods
inferred← citeshttps://doi.org/10.1016/j.bbrc.2024.151240openalex-snapshot
Topology-based protein classification: A deep learning approach
inferred← citeshttps://doi.org/10.1016/j.crstbi.2023.100108openalex-snapshot
Structural similarities between SAM and ATP recognition motifs and detection of ATP binding in a SAM binding DNA methyltransferase
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2026.150087openalex-snapshot
Decoding the full chemical catalytic cycle of class I PHA synthase: A QM/MM metadynamics perspective
inferred← citeshttps://doi.org/10.1016/j.jmb.2019.05.024openalex-snapshot
Updates to Binding MOAD (Mother of All Databases): Polypharmacology Tools and Their Utility in Drug Repurposing
inferred← citeshttps://doi.org/10.1016/j.sbi.2026.103401openalex-snapshot
Predicting targets and off-targets of small molecule drugs
inferred← citeshttps://doi.org/10.1021/acs.jafc.3c00896openalex-snapshot
Identification of Fungal and Bacterial Denitrification Inhibitors Targeting Copper Nitrite Reductase
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c01354openalex-snapshot
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.2c00895openalex-snapshot
Holo Protein Conformation Generation from Apo Structures by Ligand Binding Site Refinement
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00967openalex-snapshot
Fast Local Alignment of Protein Pockets (FLAPP): A System-Compiled Program for Large-Scale Binding Site Alignment
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00416openalex-snapshot
CHARMM-GUI-Based Induced Fit Docking Workflow to Generate Reliable Protein–Ligand Binding Modes
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/acs.jmedchem.6c01050openalex-snapshot
Mapping Non-Homologous Pocket Compatibilities to Identify Hidden Drug-Target Relationships: A Pocket Hopping Framework
inferred← citeshttps://doi.org/10.1021/acs.jpcb.5c05745openalex-snapshot
Neuronal Stimulant Dipolar Molecule Solvation Fluctuation in a Nanostructured and Confined Environment of the Lipid Bilayer: A Dynamic Disordered Rate Process Disrupting the Cell Membrane
inferred← citeshttps://doi.org/10.1038/s41598-020-61860-zopenalex-snapshot
Improving detection of protein-ligand binding sites with 3D segmentation
inferred← citeshttps://doi.org/10.1038/s41598-024-56893-7openalex-snapshot
VirtuousPocketome: a computational tool for screening protein–ligand complexes to identify similar binding sites
inferred← citeshttps://doi.org/10.1063/5.0331000openalex-snapshot
Fluorescence microscopy imaging and molecular dynamics simulation studies on methylamphetamine solvation fluctuation disturbing lipid bilayer integrity and permeability
inferred← citeshttps://doi.org/10.1080/07391102.2023.2196695openalex-snapshot
Pharmacophore-guided drug design using LdNMT as a model drug target for leishmaniasis
inferred← citeshttps://doi.org/10.1093/bib/bbac198openalex-snapshot
Computational methods to assist in the discovery of pharmacological chaperones for rare diseases
inferred← citeshttps://doi.org/10.1093/bib/bby061openalex-snapshot
Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa094openalex-snapshot
BionoiNet: ligand-binding site classification with off-the-shelf deep neural network
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/gkac402openalex-snapshot
GrAfSS: a webserver for substructure similarity searching and comparisons in the structures of proteins and RNA
inferred← citeshttps://doi.org/10.1101/2021.12.06.471420openalex-snapshot
Graphsite: Ligand-binding site classification using Deep Graph Neural Network
inferred← citeshttps://doi.org/10.1101/2025.05.24.655967openalex-snapshot
Characterizing antibodies binding to the same epitope reveals limited contribution by heavy chain CDR3 sequences relative to other CDRs
inferred← citeshttps://doi.org/10.1109/icaice68195.2025.11382290openalex-snapshot
Addressing Data Imbalance in the Prediction of Protein Binding Pocket Similarity
inferred← citeshttps://doi.org/10.1186/s12859-023-05297-xopenalex-snapshot
HLA-Clus: HLA class I clustering based on 3D structure
inferred← citeshttps://doi.org/10.1186/s13321-021-00567-3openalex-snapshot
Unexpected similarity between HIV-1 reverse transcriptase and tumor necrosis factor binding sites revealed by computer vision
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1006718openalex-snapshot
DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1009901openalex-snapshot
SiteMotif: A graph-based algorithm for deriving structural motifs in Protein Ligand binding sites
inferred← citeshttps://doi.org/10.3389/fphar.2022.855792openalex-snapshot
A New Strategy for Multitarget Drug Discovery/Repositioning Through the Identification of Similar 3D Amino Acid Patterns Among Proteins Structures: The Case of Tafluprost and its Effects on Cardiac Ion Channels
inferred← citeshttps://doi.org/10.3390/biom12081053openalex-snapshot
GraphSite: Ligand Binding Site Classification with Deep Graph Learning
inferred← citeshttps://doi.org/10.3390/ijms232012462openalex-snapshot
Estimating the Similarity between Protein Pockets
inferred← citeshttps://doi.org/10.3390/molecules23092303openalex-snapshot
Prediction Methods of Herbal Compounds in Chinese Medicinal Herbs
inferred← citeshttps://doi.org/10.3410/f.736506713.793564542openalex-snapshot
Faculty Opinions recommendation of Updates to binding MOAD (mother of all databases): polypharmacology tools and their utility in drug repurposing.
inferred← citeshttps://doi.org/10.4018/ijqspr.290010openalex-snapshot
De-Novo Design of Hits Against New Delhi Metallo-β-Lactamase Enzyme
inferred← citeshttps://doi.org/10.4049/jimmunol.2200685openalex-snapshot
HLA Class I Supertype Classification Based on Structural Similarity
inferred← citeshttps://doi.org/10.6084/m9.figshare.17073495openalex-snapshot
Additional file 1 of Unexpected similarity between HIV-1 reverse transcriptase and tumor necrosis factor binding sites revealed by computer vision
inferred← citeshttps://doi.org/10.6084/m9.figshare.22792688openalex-snapshot
Additional file 1 of HLA-Clus: HLA class I clustering based on 3D structure
inferred← citeshttps://doi.org/10.6084/m9.figshare.22792691openalex-snapshot
Additional file 2 of HLA-Clus: HLA class I clustering based on 3D structure
inferred← citeshttps://doi.org/10.64898/2025.12.30.696741openalex-snapshot
Bento: Benchmarking Classical and AI Docking on Drug Design–Relevant Data
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