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Structural and Functional View of Polypharmacology
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Functional Modules in Biological Signalling Networks
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Biological Networks and Drug Discovery—Where Do We Stand?
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Estimating the number of protein folds and families from complete genome data 1 1Edited by J. Thornton
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ggplot2: Elegant Graphics for Data Analysis
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Systems biology for molecular life sciences and its impact in biomedicine
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Protein structure alignment
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Functional site plasticity in domain superfamilies
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Analysis of Chemical and Biological Features Yields Mechanistic Insights into Drug Side Effects
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Systems biology in drug discovery and development
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Structure and dynamics of molecular networks: A novel paradigm of drug discovery
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Can we rationally design promiscuous drugs?
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Lean Big Data integration in systems biology and systems pharmacology
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SCOP: A structural classification of proteins database for the investigation of sequences and structures
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CATH – a hierarchic classification of protein domain structures
inferredcites →https://doi.org/10.1016/s1359-6446(05)03666-4openalex-snapshot
The druggable genome: an update
inferredcites →https://doi.org/10.1021/cb3001028openalex-snapshot
Rethinking Molecular Similarity: Comparing Compounds on the Basis of Biological Activity
inferredcites →https://doi.org/10.1021/ci1003637openalex-snapshot
Polypharmacology Directed Compound Data Mining: Identification of Promiscuous Chemotypes with Different Activity Profiles and Comparison to Approved Drugs
inferredcites →https://doi.org/10.1021/ci100476qopenalex-snapshot
Extracting Sets of Chemical Substructures and Protein Domains Governing Drug-Target Interactions
inferredcites →https://doi.org/10.1021/jm100574mopenalex-snapshot
Understanding and Predicting Druggability. A High-Throughput Method for Detection of Drug Binding Sites
inferredcites →https://doi.org/10.1021/jm401411zopenalex-snapshot
Molecular Similarity in Medicinal Chemistry
inferredcites →https://doi.org/10.1021/jm5006463openalex-snapshot
Polypharmacology: Challenges and Opportunities in Drug Discovery
inferredcites →https://doi.org/10.1038/35011540openalex-snapshot
From molecular to modular cell biology
inferredcites →https://doi.org/10.1038/35075138openalex-snapshot
Lethality and centrality in protein networks
inferredcites →https://doi.org/10.1038/75556openalex-snapshot
Gene Ontology: tool for the unification of biology
inferredcites →https://doi.org/10.1038/msb4100129openalex-snapshot
Network‐based prediction of protein function
inferredcites →https://doi.org/10.1038/nature01256openalex-snapshot
The structure of the protein universe and genome evolution
inferredcites →https://doi.org/10.1038/nbt.2106openalex-snapshot
Three-dimensional reconstruction of protein networks provides insight into human genetic disease
inferredcites →https://doi.org/10.1038/nbt0908-983openalex-snapshot
Data completeness—the Achilles heel of drug-target networks
inferredcites →https://doi.org/10.1038/nbt1284openalex-snapshot
Relating protein pharmacology by ligand chemistry
inferredcites →https://doi.org/10.1038/nchembio.118openalex-snapshot
Network pharmacology: the next paradigm in drug discovery
inferredcites →https://doi.org/10.1038/ncomms13542openalex-snapshot
Defining functional interactions during biogenesis of epithelial junctions
inferredcites →https://doi.org/10.1038/nmeth.2340openalex-snapshot
A large-scale evaluation of computational protein function prediction
inferredcites →https://doi.org/10.1038/nmeth.2728openalex-snapshot
Using networks to measure similarity between genes: association index selection
inferredcites →https://doi.org/10.1038/npjsba.2015.5openalex-snapshot
Elucidation of the molecular mechanisms underlying adverse reactions associated with a kinase inhibitor using systems toxicology
inferredcites →https://doi.org/10.1038/nrc2787openalex-snapshot
Targeting the cancer kinome through polypharmacology
inferredcites →https://doi.org/10.1038/nrclinonc.2012.245openalex-snapshot
Safety and feasibility of targeted agent combinations in solid tumours
inferredcites →https://doi.org/10.1038/nrd.2016.230openalex-snapshot
A comprehensive map of molecular drug targets
inferredcites →https://doi.org/10.1038/nrd3478openalex-snapshot
Trends in the exploitation of novel drug targets
inferredcites →https://doi.org/10.1039/c1mb05364gopenalex-snapshot
Promiscuous domains: facilitating stability of the yeast protein–protein interaction network
inferredcites →https://doi.org/10.1039/c2ra01345bopenalex-snapshot
Many structurally related drugs bind different targets whereas distinct drugs display significant target overlap
inferredcites →https://doi.org/10.1091/mbc.e13-04-0221openalex-snapshot
Integration of biological data by kernels on graph nodes allows prediction of new genes involved in mitotic chromosome condensation
inferredcites →https://doi.org/10.1093/bioinformatics/17.1.83openalex-snapshot
ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources
inferredcites →https://doi.org/10.1093/bioinformatics/17.suppl_1.s83openalex-snapshot
An insight into domain combinations
inferredcites →https://doi.org/10.1093/bioinformatics/btl158openalex-snapshot
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btm087openalex-snapshot
A new method to measure the semantic similarity of GO terms
inferredcites →https://doi.org/10.1093/bioinformatics/btq064openalex-snapshot
GOSemSim: an R package for measuring semantic similarity among GO terms and gene products
inferredcites →https://doi.org/10.1093/bioinformatics/btt321openalex-snapshot
Insights into polypharmacology from drug-domain associations
inferredcites →https://doi.org/10.1093/bioinformatics/btt628openalex-snapshot
The functional therapeutic chemical classification system
inferredcites →https://doi.org/10.1093/bioinformatics/btu688openalex-snapshot
IntSide: a web server for the chemical and biological examination of drug side effects
inferredcites →https://doi.org/10.1093/bioinformatics/btu711openalex-snapshot
PPDMs—a resource for mapping small molecule bioactivities from ChEMBL to Pfam-A protein domains
inferredcites →https://doi.org/10.1093/bioinformatics/btv398openalex-snapshot
Functional classification of CATH superfamilies: a domain-based approach for protein function annotation
inferredcites →https://doi.org/10.1093/jnci/djv292openalex-snapshot
Benefit, Risk, and Outcomes in Drug Development: A Systematic Review of Sunitinib
inferredcites →https://doi.org/10.1093/nar/gkp1049openalex-snapshot
GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains
inferredcites →https://doi.org/10.1093/nar/gkp987openalex-snapshot
Gene3D: merging structure and function for a Thousand genomes
inferredcites →https://doi.org/10.1093/nar/gkq973openalex-snapshot
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
inferredcites →https://doi.org/10.1093/nar/gkr1181openalex-snapshot
Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis
inferredcites →https://doi.org/10.1093/nar/gkr997openalex-snapshot
IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins
inferredcites →https://doi.org/10.1093/nar/gkt1031openalex-snapshot
The ChEMBL bioactivity database: an update
inferredcites →https://doi.org/10.1093/nar/gkt1223openalex-snapshot
Pfam: the protein families database
inferredcites →https://doi.org/10.1093/nar/gku1003openalex-snapshot
STRING v10: protein–protein interaction networks, integrated over the tree of life
inferredcites →https://doi.org/10.1093/nar/gku1113openalex-snapshot
The GOA database: Gene Ontology annotation updates for 2015
inferredcites →https://doi.org/10.1093/nar/gku947openalex-snapshot
CATH: comprehensive structural and functional annotations for genome sequences
inferredcites →https://doi.org/10.1093/nar/gkv1075openalex-snapshot
The SIDER database of drugs and side effects
inferredcites →https://doi.org/10.1097/jto.0b013e3181e981d9openalex-snapshot
Side-Effects of Long-Term Administration of Erlotinib in Patients with Non-small Cell Lung Cancer
inferredcites →https://doi.org/10.1126/science.1085371openalex-snapshot
Evolution of the Protein Repertoire
inferredcites →https://doi.org/10.1126/science.1158140openalex-snapshot
Drug Target Identification Using Side-Effect Similarity
inferredcites →https://doi.org/10.1126/science.1257601openalex-snapshot
Uncovering disease-disease relationships through the incomplete interactome
inferredcites →https://doi.org/10.1146/annurev-pharmtox-010611-134520openalex-snapshot
Systems Pharmacology: Network Analysis to Identify Multiscale Mechanisms of Drug Action
inferredcites →https://doi.org/10.1146/annurev-pharmtox-011613-135943openalex-snapshot
The Druggable Genome: Evaluation of Drug Targets in Clinical Trials Suggests Major Shifts in Molecular Class and Indication
inferredcites →https://doi.org/10.1186/1471-2105-10-168openalex-snapshot
Fpocket: An open source platform for ligand pocket detection
inferredcites →https://doi.org/10.1186/1471-2105-10-39openalex-snapshot
Protein domain organisation: adding order
inferredcites →https://doi.org/10.1186/1471-2105-13-s17-s11openalex-snapshot
Mapping small molecule binding data to structural domains
inferredcites →https://doi.org/10.1186/1471-2105-13-s6-s11openalex-snapshot
Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data
inferredcites →https://doi.org/10.1186/1471-2105-14-s3-s5openalex-snapshot
Protein function prediction using domain families
inferredcites →https://doi.org/10.1186/1471-2105-14-s4-s5openalex-snapshot
Bioinformatics analysis of the epitope regions for norovirus capsid protein
inferredcites →https://doi.org/10.1186/1752-0509-7-90openalex-snapshot
Topology of molecular interaction networks
inferredcites →https://doi.org/10.1186/s13059-016-1037-6openalex-snapshot
An expanded evaluation of protein function prediction methods shows an improvement in accuracy
inferredcites →https://doi.org/10.1208/s12248-012-9392-zopenalex-snapshot
Rationalizing Structure and Target Relationships between Current Drugs
inferredcites →https://doi.org/10.1371/journal.pcbi.0030059openalex-snapshot
The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics
inferredcites →https://doi.org/10.1371/journal.pcbi.1000945openalex-snapshot
Finding the “Dark Matter” in Human and Yeast Protein Network Prediction and Modelling
inferredcites →https://doi.org/10.1371/journal.pcbi.1003119openalex-snapshot
Target Essentiality and Centrality Characterize Drug Side Effects
inferredcites →https://doi.org/10.1371/journal.pcbi.1004024openalex-snapshot
Analysis of Individual Protein Regions Provides Novel Insights on Cancer Pharmacogenomics
inferredcites →https://doi.org/10.1371/journal.pone.0008918openalex-snapshot
Automated Network Analysis Identifies Core Pathways in Glioblastoma
inferredcites →https://doi.org/10.1586/14737140.7.9.1183openalex-snapshot
Lapatinib in the treatment of breast cancer
inferredcites →https://doi.org/10.1634/theoncologist.9-90005-10openalex-snapshot
The Role of Hypoxia-Induced Factors in Tumor Progression
inferredcites →https://doi.org/10.1634/theoncologist.9-suppl_3-10openalex-snapshot
Dual Kinase Inhibition in the Treatment of Breast Cancer: Initial Experience with the EGFR/ErbB-2 Inhibitor Lapatinib
inferredcites →https://doi.org/10.2165/00002018-200932090-00003openalex-snapshot
Benefit-Risk Assessment of Sunitinib in Gastrointestinal Stromal Tumours and Renal Cancer
inferredcites →https://doi.org/10.2174/157016461103140922164228openalex-snapshot
Oncogenic Signalling Networks and Polypharmacology as Paradigms to Cope with Cancer Heterogeneity
inferredcites →https://doi.org/10.25080/tcwv9851openalex-snapshot
Exploring Network Structure, Dynamics, and Function using NetworkX
inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot
R: A Language and Environment for Statistical Computing
inferredcites →https://doi.org/10.3389/fphys.2016.00375openalex-snapshot
Evolution of Centrality Measurements for the Detection of Essential Proteins in Biological Networks
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1007/978-1-4939-6783-4_4openalex-snapshot
CATH-Gene3D: Generation of the Resource and Its Use in Obtaining Structural and Functional Annotations for Protein Sequences
inferred← citeshttps://doi.org/10.1038/s41386-022-01406-1openalex-snapshot
Integrating human brain proteomic data with genome-wide association study findings identifies novel brain proteins in substance use traits
inferred← citeshttps://doi.org/10.1038/s41593-021-00832-6openalex-snapshot
Brain proteome-wide association study implicates novel proteins in depression pathogenesis
inferred← citeshttps://doi.org/10.12688/f1000research.11517.1openalex-snapshot
A simple mathematical approach to the analysis of polypharmacology and polyspecificity data
inferred← citeshttps://doi.org/10.1556/650.2020.31703openalex-snapshot
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