Research graph
References from Current computational methods for predicting protein interactions of natural products. Local targets link to admitted publications; unresolved targets remain external evidence.
Computational studies and biosynthesis of natural products with promising anticancer properties
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Are we seeing a resurgence in the use of natural products for new drug discovery?
2019 · External reference
Unresolved reference
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10.1093/nar/gkv1319
10.1093/nar/gkv1319 · External reference
NANPDB: a resource for natural products from Northern African sources
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From one Nobel Prize (P. Ehrlich) to another (Tu Youyou): 100 years of chemotherapy of infectious diseases
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10.1021/jm5006463 · External reference
Shifting from the single to the multitarget paradigm in drug discovery
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10.1016/j.drudis.2015.12.007
10.1016/j.drudis.2015.12.007 · External reference
Target fishing by cross-docking to explain polypharmacological effects
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Reverse screening methods to search for the protein targets of chemopreventive compounds
10.3389/fchem.2018.00138 · 2018 · External reference
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Molecular similarity: a key technique in molecular informatics
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Molecular similarity in medicinal chemistry
10.1021/jm401411z · 2014 · External reference
Über den jetzigen Stand der Chemotherapie
1908 · External reference
Pharmacophore definition and 3D searches
10.1016/j.ddtec.2004.11.015 · 2004 · External reference
Glossary of terms used in medicinal chemistry (IUPAC Recommendations 1998)
10.1351/pac199870051129 · 1998 · External reference
Parallel screening: a novel concept in pharmacophore modeling and virtual screening
10.1021/ci6002043 · 2006 · External reference
Common pharmacophore identification using frequent clique detection algorithm
10.1021/ci8002478 · 2009 · External reference
History of 3D pharmacophore searching: commercial, academic and open-source tools
10.1016/j.ddtec.2010.12.002 · 2010 · External reference
Performance evaluation of 2D fingerprint and 3D shape similarity methods in virtual screening
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10.1016/j.ddtec.2010.11.004
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10.1021/ci2005274 · External reference
Pharmer: efficient and exact pharmacophore search
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Unresolved reference
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10.1021/ci049885e
10.1021/ci049885e · External reference
PHASE: a novel approach to pharmacophore modeling and 3D database searching
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Unresolved reference
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Unresolved reference
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ZINCPharmer: pharmacophore search of the ZINC database
10.1093/nar/gks378 · 2012 · External reference
PharmMapper 2017 update: a web server for potential drug target identification with a comprehensive target pharmacophore database
10.1093/nar/gkx374 · 2017 · External reference
Pharmit: interactive exploration of chemical space
10.1093/nar/gkw287 · 2016 · External reference
10.1093/nar/gky380
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In silico workflow for the discovery of natural products activating the G protein-coupled bile acid receptor 1
10.3389/fchem.2018.00242 · 2018 · External reference
Receptor-based pharmacophore and pharmacophore key descriptors for virtual screening and QSAR modeling
10.2174/157340911796504332 · 2011 · External reference
Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation
10.1007/s10822-009-9268-1 · 2009 · External reference
Protein−ligand-based pharmacophores: generation and utility assessment in computational ligand profiling
10.1021/ci300083r · 2012 · External reference
Unresolved reference
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In silico target fishing for rationalized ligand discovery exemplified on constituents of Ruta graveolens
10.1055/s-0028-1088397 · 2009 · External reference
Implementation of nearest-neighbor searching in an online chemical structure search system
1986 · External reference
Chemical similarity using geometric atom pair descriptors
10.1021/ci950275b · 1996 · External reference
Open-source platform to benchmark fingerprints for ligand-based virtual screening
10.1186/1758-2946-5-26 · 2013 · External reference
Comparing structural fingerprints using a literature-based similarity benchmark
10.1186/s13321-016-0148-0 · 2016 · External reference
10.1016/j.ymeth.2014.08.005
10.1016/j.ymeth.2014.08.005 · External reference
On the properties of bit string-based measures of chemical similarity
1998 · External reference
10.1198/004017002317375064
10.1198/004017002317375064 · External reference
10.5936/csbj.201302002
10.5936/csbj.201302002 · External reference
Why is Tanimoto index an appropriate choice for fingerprint-based similarity calculations?
10.1186/s13321-015-0069-3 · 2015 · External reference
Activity-relevant similarity values for fingerprints and implications for similarity searching
10.12688/f1000research.8357.1 · 2016 · External reference
Do structurally similar molecules have similar biological activity?
10.1021/jm020155c · 2002 · External reference
SwissSimilarity: a web tool for low to ultra high throughput ligand-based virtual screening
10.1021/acs.jcim.6b00174 · 2016 · External reference
SuperPred: drug classification and target prediction
10.1093/nar/gkn307 · 2008 · External reference
10.1208/s12248-012-9449-z
10.1208/s12248-012-9449-z · External reference
HybridSim-VS: a web server for large-scale ligand-based virtual screening using hybrid similarity recognition techniques
10.1093/bioinformatics/btx418 · 2017 · External reference
Multi-targeted natural products evaluation based on biological activity prediction with PASS
10.2174/138161210791164063 · 2010 · External reference
10.1038/nbt1284
10.1038/nbt1284 · External reference
USR-VS: a web server for large-scale prospective virtual screening using ultrafast shape recognition techniques
10.1093/nar/gkw320 · 2016 · External reference
10.1016/j.jmgm.2016.08.001
10.1016/j.jmgm.2016.08.001 · External reference
Miconidin acetate and primin as potent 5-lipoxygenase inhibitors from brazilian eugenia hiemalis (Myrtaceae)
10.1055/s-0042-102460 · 2016 · External reference
The correlation of biological activity of plant growth regulators and chloromycetin derivatives with hammett constants and partition coefficients
10.1021/ja00901a033 · 1963 · External reference
QSAR and its role in target-ligand interaction
10.2174/1875036201307010063 · 2013 · External reference
10.1016/j.drudis.2018.05.010
10.1016/j.drudis.2018.05.010 · External reference
Receptor dependent multidimensional QSAR for modeling drug–receptor interactions
10.2174/092986709788803286 · 2009 · External reference
Multi-dimensional QSAR in drug discovery
10.1016/j.drudis.2007.08.004 · 2007 · External reference
QSAR Modeling: where have you been? Where are you going to?
2013 · External reference
Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins
10.1021/ja00226a005 · 1988 · External reference
Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity
10.1021/jm00050a010 · 1994 · External reference
Unresolved reference
2011 · External reference
Compass: predicting biological activities from molecular surface properties. Performance comparisons on a steroid benchmark
10.1021/jm00041a010 · 1994 · External reference
Comparative molecular moment analysis (coMMA): 3D-QSAR without molecular superposition
10.1021/jm950589q · 1996 · External reference
Molecular hologram QSAR
2009 · External reference
GRid-INdependent descriptors (GRIND): a novel class of alignment-independent three-dimensional molecular descriptors
10.1021/jm000941m · 2000 · External reference
Suitability of GRIND-based principal properties for the description of molecular similarity and ligand-based virtual screening
10.1021/ci900228x · 2009 · External reference
10.4155/fmc-2016-0093
10.4155/fmc-2016-0093 · External reference
Prediction of drug binding affinities by comparative binding energy analysis
10.1021/jm00014a020 · 1995 · External reference
10.1021/jm020808p
10.1021/jm020808p · External reference
10.1016/j.jprot.2011.05.011
10.1016/j.jprot.2011.05.011 · External reference
Combining QSAR classification models for predictive modeling of human monoamine oxidase inhibitors
10.1016/j.ejmech.2012.10.035 · 2013 · External reference
Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors
10.1002/1521-3773(20020802)41:15<2644::aid-anie2644>3.0.co;2-o · 2002 · External reference
10.1007/s12551-016-0247-1
10.1007/s12551-016-0247-1 · External reference
10.1016/j.cell.2015.03.050
10.1016/j.cell.2015.03.050 · External reference
Homology modeling in drug discovery: overview, current applications, and future perspectives
10.1111/cbdd.13388 · 2019 · External reference
10.1021/jm050362n
10.1021/jm050362n · External reference
10.1146/annurev.biophys.36.040306.132550
10.1146/annurev.biophys.36.040306.132550 · External reference
Forging the basis for developing protein-ligand interaction scoring functions
10.1021/acs.accounts.6b00491 · 2017 · External reference
Empirical scoring functions for structure-based virtual screening: applications, critical aspects, and challenges
10.3389/fphar.2018.01089 · 2018 · External reference
10.1021/jm990352k
10.1021/jm990352k · External reference
Machine learning consensus scoring improves performance across targets in structure-based virtual screening
10.1021/acs.jcim.7b00153 · 2017 · External reference
Machine learning in computational docking
10.1016/j.artmed.2015.02.002 · 2015 · External reference
Performance of machine-learning scoring functions in structure-based virtual screening
10.1038/srep46710 · 2017 · External reference
A machine learning approach to predicting protein–ligand binding affinity with applications to molecular docking
10.1093/bioinformatics/btq112 · 2010 · External reference
The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities
10.1517/17460441.2015.1032936 · 2015 · External reference
10.1002/minf.201100135
10.1002/minf.201100135 · External reference
10.1021/ci100275a
10.1021/ci100275a · External reference
Induced fit docking, and the use of QM/MM methods in docking
10.1016/j.ddtec.2013.02.003 · 2013 · External reference
10.1006/jmbi.1996.0897
10.1006/jmbi.1996.0897 · External reference
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10.1021/jm0306430 · External reference
10.1006/jmbi.1996.0477
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TarFisDock: a web server for identifying drug targets with docking approach
10.1093/nar/gkl114 · 2006 · External reference
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10.1093/nar/gks496
10.1093/nar/gks496 · External reference
In vitro and in silico evaluation of stereoselective effect of ginsenoside isomers on platelet P2Y12 receptor
2019 · External reference
In silico investigation of the anti-tumor mechanisms of epigallocatechin-3-gallate
2019 · External reference
10.1002/jcc.21334
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10.1016/j.tibtech.2008.01.004
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Graph-based methods for analysing networks in cell biology
10.1093/bib/bbl022 · 2006 · External reference
Network-based methods for prediction of drug-target interactions
10.3389/fphar.2018.01134 · 2018 · External reference
DrugBank 5.0: a major update to the DrugBank database for 2018
2017 · External reference
10.1093/nar/gkw1074
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PubChem BioAssay: 2017 update
10.1093/nar/gkw1118 · 2016 · External reference
BindingDB in 2015: a public database for medicinal chemistry, computational chemistry and systems pharmacology
10.1093/nar/gkv1072 · 2016 · External reference
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Predicting drug-target interactions for new drug compounds using a weighted nearest neighbor profile
10.1371/journal.pone.0066952 · 2013 · External reference
Prediction of drug-target interaction networks from the integration of chemical and genomic spaces
10.1093/bioinformatics/btn162 · 2008 · External reference
Machine intelligence decrypts β-lapachone as an allosteric 5-lipoxygenase inhibitor
10.1039/c8sc02634c · 2018 · External reference
Semi-supervised drug-protein interaction prediction from heterogeneous biological spaces
10.1186/1752-0509-4-s2-s6 · 2010 · External reference
Discovery of a novel inhibitor of the hedgehog signaling pathway through cell-based compound discovery and target prediction
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Repurposing de novo designed entities reveals phosphodiesterase 3B and cathepsin L modulators
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De-orphaning the marine natural product (±)-marinopyrrole A by computational target prediction and biochemical validation
10.1039/c6cc09693j · 2017 · External reference
Design of natural-product-inspired multitarget ligands by machine learning
10.1002/cmdc.201900097 · 2019 · External reference
Modelling ligand selectivity of serine proteases using integrative proteochemometric approaches improves model performance and allows the multi-target dependent interpretation of features
10.1039/c4ib00175c · 2014 · External reference
Polypharmacology modelling using proteochemometrics (PCM): recent methodological developments, applications to target families, and future prospects
2014 · External reference
10.1186/s13321-015-0063-9
10.1186/s13321-015-0063-9 · External reference
Proteochemometric mapping of the interaction of organic compounds with melanocortin receptor subtypes
10.1124/mol.104.002857 · 2004 · External reference
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Proteochemometrics modeling of the interaction of amine G-protein coupled receptors with a diverse set of ligands
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QSAR and proteo-chemometric analysis of the interaction of a series of organic compounds with melanocortin receptor subtypes
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Unbiased descriptor and parameter selection confirms the potential of proteochemometric modelling
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Proteochemometric modeling of the bioactivity spectra of HIV-1 protease inhibitors by introducing protein-ligand interaction fingerprint
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