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Improving the performance of the PLB index for ligand-binding site prediction using dihedral angles and the solvent-accessible surface area

https://doi.org/10.1038/srep33232
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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.10484openalex-snapshot
Analysis of protein structures reveals regions of rare backbone conformation at functional sites
inferredcites →https://doi.org/10.1002/prot.20305openalex-snapshot
The ConSurf‐HSSP database: The mapping of evolutionary conservation among homologs onto PDB structures
inferredcites →https://doi.org/10.1002/prot.20769openalex-snapshot
A method for localizing ligand binding pockets in protein structures
inferredcites →https://doi.org/10.1006/jmbi.1994.1334openalex-snapshot
Satisfying Hydrogen Bonding Potential in Proteins
inferredcites →https://doi.org/10.1016/0263-7855(95)00073-9openalex-snapshot
SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions
inferredcites →https://doi.org/10.1016/j.drudis.2010.05.015openalex-snapshot
Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery
inferredcites →https://doi.org/10.1016/s1093-3263(98)00002-3openalex-snapshot
LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins
inferredcites →https://doi.org/10.1021/ci400541dopenalex-snapshot
Dihedral-Based Segment Identification and Classification of Biopolymers I: Proteins
inferredcites →https://doi.org/10.1021/ci6002202openalex-snapshot
Use of Amino Acid Composition to Predict Ligand-Binding Sites
inferredcites →https://doi.org/10.1021/ci7002363openalex-snapshot
Identification of the Druggable Concavity in Homology Models Using the PLB Index
inferredcites →https://doi.org/10.1023/a:1008124202956openalex-snapshot
Fast prediction and visualization of protein binding pockets with PASS
inferredcites →https://doi.org/10.1038/nprot.2015.043openalex-snapshot
The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins
inferredcites →https://doi.org/10.1073/pnas.1117768109openalex-snapshot
The distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation
inferredcites →https://doi.org/10.1074/mcp.m400159-mcp200openalex-snapshot
Pocketome via Comprehensive Identification and Classification of Ligand Binding Envelopes
inferredcites →https://doi.org/10.1089/omi.2009.0045openalex-snapshot
MetaPocket: A Meta Approach to Improve Protein Ligand Binding Site Prediction
inferredcites →https://doi.org/10.1093/bioinformatics/bti315openalex-snapshot
Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites
inferredcites →https://doi.org/10.1093/bioinformatics/btm537openalex-snapshot
Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting
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/btr331openalex-snapshot
Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction
inferredcites →https://doi.org/10.1093/bioinformatics/bts182openalex-snapshot
Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles
inferredcites →https://doi.org/10.1093/nar/25.17.3389openalex-snapshot
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot
The Protein Data Bank
inferredcites →https://doi.org/10.1093/nar/29.13.2860openalex-snapshot
Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level
inferredcites →https://doi.org/10.1093/nar/gkl282openalex-snapshot
CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
inferredcites →https://doi.org/10.1093/nar/gkl842openalex-snapshot
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
inferredcites →https://doi.org/10.1093/nar/gkm911openalex-snapshot
Binding MOAD, a high-quality protein ligand database
inferredcites →https://doi.org/10.1093/nar/gkp281openalex-snapshot
SITEHOUND-web: a server for ligand binding site identification in protein structures
inferredcites →https://doi.org/10.1093/nar/gku321openalex-snapshot
GalaxySite: ligand-binding-site prediction by using molecular docking
inferredcites →https://doi.org/10.1109/tcbb.2013.104openalex-snapshot
Designing Template-Free Predictor for Targeting Protein-Ligand Binding Sites with Classifier Ensemble and Spatial Clustering
inferredcites →https://doi.org/10.1155/2015/757495openalex-snapshot
Amino Acids in Nine Ligand-Prefer Ramachandran Regions
inferredcites →https://doi.org/10.1186/1471-2105-15-s15-s4openalex-snapshot
LigandRFs: random forest ensemble to identify ligand-binding residues from sequence information alone
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/10.1186/1752-153x-1-7openalex-snapshot
PocketPicker: analysis of ligand binding-sites with shape descriptors
inferredcites →https://doi.org/10.1208/s12248-012-9426-6openalex-snapshot
Pocket-Based Drug Design: Exploring Pocket Space
inferredcites →https://doi.org/10.1371/journal.pcbi.1000585openalex-snapshot
Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure
inferredcites →https://doi.org/10.1529/biophysj.107.114280openalex-snapshot
M-TASSER: An Algorithm for Protein Quaternary Structure Prediction

What points at this work

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

inferred← citeshttps://doi.org/10.1016/j.jphotochem.2025.116806openalex-snapshot
Interaction mechanism of nano-curcumin induced by oil-in-water method with α-crystalline: Assessments through spectroscopy and molecular simulation techniques
inferred← citeshttps://doi.org/10.1021/jacs.4c12716openalex-snapshot
Unraveling Hydration Shell Dynamics and Viscosity Effects Around Cyanamide Probes via 2D IR Spectroscopy
inferred← citeshttps://doi.org/10.1073/pnas.2221967120openalex-snapshot
Design of rigid protein–protein interaction inhibitors enables targeting of undruggable Mcl-1
inferred← citeshttps://doi.org/10.1080/07391102.2024.2333449openalex-snapshot
A unique approach for protein secondary structure comparison under TOPS representation
inferred← citeshttps://doi.org/10.1093/bib/bbad115openalex-snapshot
MetaHMEI: meta-learning for prediction of few-shot histone modifying enzyme inhibitors
inferred← citeshttps://doi.org/10.1093/gigascience/giag010openalex-snapshot
ViralBindPredict: empowering viral protein–ligand binding sites through deep learning and protein sequence-derived insights
inferred← citeshttps://doi.org/10.1186/s12859-018-2065-xopenalex-snapshot
RaptorX-Angle: real-value prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning
inferred← citeshttps://doi.org/10.3389/fbioe.2020.00493openalex-snapshot
Recognizing Ion Ligand–Binding Residues by Random Forest Algorithm Based on Optimized Dihedral Angle
inferred← citeshttps://doi.org/10.3390/ijms20102499openalex-snapshot
Fragment-Based Ligand-Protein Contact Statistics: Application to Docking Simulations
inferred← citeshttps://doi.org/10.3390/molecules22101673openalex-snapshot
Systematic Identification of Machine-Learning Models Aimed to Classify Critical Residues for Protein Function from Protein Structure
inferred← citeshttps://doi.org/10.48550/arxiv.1712.07244openalex-snapshot
Real-value and confidence prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning
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