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Similarity networks of protein binding sites
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1 of the 41 references listed on this page is in the Retraction Watch database as retracted (export 2026-11-11): 10.1126/science.1098432 (notice 2008-02-01).
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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/pro.5560061104openalex-snapshot
Tess: A geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites
inferredcites →https://doi.org/10.1002/prot.10339openalex-snapshot
A new bioinformatic approach to detect common 3D sites in protein structures
inferredcites →https://doi.org/10.1006/jmbi.1994.1657openalex-snapshot
A Graph-theoretic Approach to the Identification of Three-dimensional Patterns of Amino Acid Side-chains in Protein Structures
inferredcites →https://doi.org/10.1006/jmbi.2000.3550openalex-snapshot
Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores
inferredcites →https://doi.org/10.1006/jmbi.2001.4526openalex-snapshot
Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast11Edited by J. Karn
inferredcites →https://doi.org/10.1006/jmbi.2001.5079openalex-snapshot
Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model
inferredcites →https://doi.org/10.1016/j.jmb.2003.08.061openalex-snapshot
Uncovering Network Systems Within Protein Structures
inferredcites →https://doi.org/10.1016/j.jmb.2004.04.012openalex-snapshot
Recognition of Functional Sites in Protein Structures
inferredcites →https://doi.org/10.1016/j.jmb.2004.06.063openalex-snapshot
The Protein Folding Network
inferredcites →https://doi.org/10.1016/j.jmb.2004.10.055openalex-snapshot
Network Analysis of Protein Structures Identifies Functional Residues
inferredcites →https://doi.org/10.1016/j.sbi.2004.05.003openalex-snapshot
Protein interaction networks from yeast to human
inferredcites →https://doi.org/10.1016/s0022-2836(02)00649-6openalex-snapshot
One Fold with Many Functions: The Evolutionary Relationships between TIM Barrel Families Based on their Sequences, Structures and Functions
inferredcites →https://doi.org/10.1016/s0022-2836(02)00811-2openalex-snapshot
A New Method to Detect Related Function Among Proteins Independent of Sequence and Fold Homology
inferredcites →https://doi.org/10.1016/s0022-2836(03)00045-7openalex-snapshot
A Model for Statistical Significance of Local Similarities in Structure
inferredcites →https://doi.org/10.1016/s0022-2836(03)00882-9openalex-snapshot
Inferring Functional Relationships of Proteins from Local Sequence and Spatial Surface Patterns
inferredcites →https://doi.org/10.1016/s0959-440x(99)80051-7openalex-snapshot
From protein structure to function
inferredcites →https://doi.org/10.1016/s1359-6446(05)03369-6openalex-snapshot
Global properties of biological networks
inferredcites →https://doi.org/10.1023/a:1026127927612openalex-snapshot
From protein structure to biochemical function?
inferredcites →https://doi.org/10.1038/30918openalex-snapshot
Collective dynamics of ‘small-world’ networks
inferredcites →https://doi.org/10.1038/ng881openalex-snapshot
Network motifs in the transcriptional regulation network of Escherichia coli
inferredcites →https://doi.org/10.1073/pnas.0407152101openalex-snapshot
The protein structure prediction problem could be solved using the current PDB library
inferredcites →https://doi.org/10.1073/pnas.202497999openalex-snapshot
Expanding protein universe and its origin from the biological Big Bang
inferredcites →https://doi.org/10.1073/pnas.85.8.2444openalex-snapshot
Improved tools for biological sequence comparison.
inferredcites →https://doi.org/10.1093/bioinformatics/btg243openalex-snapshot
Protein Ligand Database (PLD): additional understanding of the nature and specificity of protein–ligand complexes
inferredcites →https://doi.org/10.1093/bioinformatics/bth113openalex-snapshot
Efficient similarity search in protein structure databases by k-clique hashing
inferredcites →https://doi.org/10.1093/bioinformatics/bti337openalex-snapshot
Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons
inferredcites →https://doi.org/10.1093/nar/gkh054openalex-snapshot
SURFACE: a database of protein surface regions for functional annotation
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a003957openalex-snapshot
Scale-Free Behavior in Protein Domain Networks
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/10.1093/protein/13.3.149openalex-snapshot
Simplified amino acid alphabets for protein fold recognition and implications for folding
inferredcites →https://doi.org/10.1101/gr.2300204openalex-snapshot
Evolution and Topology in the Yeast Protein Interaction Network
inferredcites →https://doi.org/10.1103/physreve.65.061910openalex-snapshot
Small-world view of the amino acids that play a key role in protein folding
inferredcites →https://doi.org/10.1110/ps.0368703openalex-snapshot
Identification of protein biochemical functions by similarity search using the molecular surface database eF‐site
inferredcites →https://doi.org/10.1126/science.1065103openalex-snapshot
Specificity and Stability in Topology of Protein Networks
inferredcites →https://doi.org/10.1126/science.1073374openalex-snapshot
Hierarchical Organization of Modularity in Metabolic Networks
inferredcites →https://doi.org/10.1126/science.1098432openalex-snapshot
Computational Design of a Biologically Active Enzyme
inferredcites →https://doi.org/10.1126/science.286.5439.509openalex-snapshot
Emergence of Scaling in Random Networks
inferredcites →https://doi.org/10.1145/362342.362367openalex-snapshot
Algorithm 457: finding all cliques of an undirected graph
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/cmdc.201600121openalex-snapshot
Comparing Drug Images and Repurposing Drugs with BioGPS and FLAPdock: The Thymidylate Synthase Case
inferred← citeshttps://doi.org/10.1002/ijch.201400013openalex-snapshot
On the Role of Physics and Evolution in Dictating Protein Structure and Function
inferred← citeshttps://doi.org/10.1002/jcc.20826openalex-snapshot
Unified QSAR and network‐based computational chemistry approach to antimicrobials, part 1: Multispecies activity models for antifungals
inferred← citeshttps://doi.org/10.1002/minf.201300082openalex-snapshot
Identification of Similar Binding Sites to Detect Distant Polypharmacology
inferred← citeshttps://doi.org/10.1002/prot.21780openalex-snapshot
Binding similarity network of ligand
inferred← citeshttps://doi.org/10.1002/prot.21858openalex-snapshot
A simple and fuzzy method to align and compare druggable ligand‐binding sites
inferred← citeshttps://doi.org/10.1002/prot.22655openalex-snapshot
Mapping of ligand‐binding cavities in proteins
inferred← citeshttps://doi.org/10.1007/978-1-4419-6045-0_19openalex-snapshot
Trends in Chemical Graph Data Mining
inferred← citeshttps://doi.org/10.1007/s00726-008-0088-8openalex-snapshot
Bridging protein local structures and protein functions
inferred← citeshttps://doi.org/10.1007/s10969-011-9110-6openalex-snapshot
Beyond structural genomics: computational approaches for the identification of ligand binding sites in protein structures
inferred← citeshttps://doi.org/10.1007/s11424-008-9143-5openalex-snapshot
Recognition of Structure Similarities in Proteins
inferred← citeshttps://doi.org/10.1007/s12013-009-9051-xopenalex-snapshot
Potential for Protein Surface Shape Analysis Using Spherical Harmonics and 3D Zernike Descriptors
inferred← citeshttps://doi.org/10.1007/s12013-016-0750-9openalex-snapshot
Active Site Characterization of Proteases Sequences from Different Species of Aspergillus
inferred← citeshttps://doi.org/10.1016/j.bmc.2008.11.007openalex-snapshot
QSAR and complex network study of the chiral HMGR inhibitor structural diversity
inferred← citeshttps://doi.org/10.1016/j.jtbi.2008.09.042openalex-snapshot
Cutoff variation induces different topological properties: A new discovery of amino acid network within protein
inferred← citeshttps://doi.org/10.1016/j.pharmthera.2013.01.016openalex-snapshot
Structure and dynamics of molecular networks: A novel paradigm of drug discovery
inferred← citeshttps://doi.org/10.1016/s1387-2656(08)00005-7openalex-snapshot
Network models in drug discovery and regenerative medicine
inferred← citeshttps://doi.org/10.1021/ci8000259openalex-snapshot
Quantifying the Relationships among Drug Classes
inferred← citeshttps://doi.org/10.1021/ci800113copenalex-snapshot
Chemocavity: Specific Concavity in Protein Reserved for the Binding of Biologically Functional Small Molecules
inferred← citeshttps://doi.org/10.1021/ci900317xopenalex-snapshot
Rapid Comparison of Protein Binding Site Surfaces with Property Encoded Shape Distributions
inferred← citeshttps://doi.org/10.1021/mp800102copenalex-snapshot
Alignment-Free Prediction of a Drug−Target Complex Network Based on Parameters of Drug Connectivity and Protein Sequence of Receptors
inferred← citeshttps://doi.org/10.1038/nchembio.118openalex-snapshot
Network pharmacology: the next paradigm in drug discovery
inferred← citeshttps://doi.org/10.1038/nrd3503openalex-snapshot
Minimum information about a bioactive entity (MIABE)
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/10.1038/sj.bjp.0707307openalex-snapshot
Chemogenomic approaches to rational drug design
inferred← citeshttps://doi.org/10.1038/srep06356openalex-snapshot
Characterizing the pocketome of Mycobacterium tuberculosis and application in rationalizing polypharmacological target selection
inferred← citeshttps://doi.org/10.1039/b901356copenalex-snapshot
Predicting the multi-modal binding propensity of small molecules: towards an understanding of drug promiscuity
inferred← citeshttps://doi.org/10.1039/c2md20242eopenalex-snapshot
On the origins of drug polypharmacology
inferred← citeshttps://doi.org/10.1073/pnas.0704422105openalex-snapshot
Detecting evolutionary relationships across existing fold space, using sequence order-independent profile–profile alignments
inferred← citeshttps://doi.org/10.1073/pnas.1300011110openalex-snapshot
Interplay of physics and evolution in the likely origin of protein biochemical function
inferred← citeshttps://doi.org/10.1073/pnas.1908241116openalex-snapshot
On the possible origin of protein homochirality, structure, and biochemical function
inferred← citeshttps://doi.org/10.1093/bioinformatics/btm470openalex-snapshot
The Poisson Index: a new probabilistic model for protein–ligand binding site similarity
inferred← citeshttps://doi.org/10.1093/bioinformatics/btp220openalex-snapshot
A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery
inferred← citeshttps://doi.org/10.1093/bioinformatics/btt024openalex-snapshot
APoc: large-scale identification of similar protein pockets
inferred← citeshttps://doi.org/10.1093/database/bau029openalex-snapshot
PLIC: protein–ligand interaction clusters
inferred← citeshttps://doi.org/10.1155/2015/843030openalex-snapshot
Development of a Machine Learning Method to Predict Membrane Protein-Ligand Binding Residues Using Basic Sequence Information
inferred← citeshttps://doi.org/10.1186/1471-2105-11-242openalex-snapshot
Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction
inferred← citeshttps://doi.org/10.1186/1471-2105-8-147openalex-snapshot
Exploiting residue-level and profile-level interface propensities for usage in binding sites prediction of proteins
inferred← citeshttps://doi.org/10.1186/s12859-018-2109-2openalex-snapshot
Comparative assessment of strategies to identify similar ligand-binding pockets in proteins
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1003302openalex-snapshot
A Comprehensive Survey of Small-Molecule Binding Pockets in Proteins
inferred← citeshttps://doi.org/10.2174/1389203711314020004openalex-snapshot
The Topology and Dynamics of Protein Complexes: Insights from Intra– Molecular Network Theory
inferred← citeshttps://doi.org/10.3389/fphar.2015.00186openalex-snapshot
Identifying problematic drugs based on the characteristics of their targets
inferred← citeshttps://doi.org/10.4155/fmc.09.11openalex-snapshot
Self-Organizing Molecular Fingerprints: A Ligand-Based View on Drug-Like Chemical Space and Off-Target Prediction
inferred← citeshttps://doi.org/10.7763/ijbbb.2013.v3.250openalex-snapshot
A Complex Network Approach for the Analysis of Protein Units Similarity Using Structural Alphabet
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