Programs

ACFISHao G.-F., Jiang W., Ye Y.-N., Wu F.-X., Zhu X.-L., Guo F.-B., Yang G.-F., ACFIS: a web server for fragment-based drug discovery. Nucleic Acids Research, 2016, 44, W550–W556. Abstract
ACIDWang F., Wu F.-X., Li C.-Z., Jia C.-Y., Su S.-W., Hao G.-F., Yang G.-F., ACID: a free tool for drug repurposing using consensus inverse docking strategy. Journal of Cheminformatics, 2019, 11, Article No 73. Abstract
Activity Landscape PlotterGonzález-Medina M., Méndez-Lucio O., Medina-Franco J. L., Activity Landscape Plotter: a web-based application for the analysis of structure–activity relationships. Journal of Chemical Information and Modeling, 2017, 57, 397–402. Abstract
ADME SARfariDavies M., Dedman N, Hersey A., Papadatos G., Hall M. D., Cucurull-Sanchez L., Jeffrey P., Hasan S., Eddershaw P. J., Overington J. P., ADME SARfari: comparative genomics of drug metabolizing systems. Bioinformatics, 2015, 31, 1695–1697. Abstract
ADMETlabDong J., Wang N.-N., Yao Z-J., Zhang L., Cheng Y., Ouyang D., Lu A.-P., Cao D.-S., ADMETlab: a platform for systematic ADMET evaluation based on a comprehensively collected ADMET database. Journal of Cheminformatics, 2018, 10, Article No 29. Abstract
ADMETlab 2.0Xiong G., Wu Z., Yi J., Fu L., Yang Z., Hsieh C., Yin M., Zeng X., Wu C., Lu A., Chen X., Hou T., Cao D., ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties. Nucleic Acids Research, 2021, 49, W5–W14. Abstract
ADMEToptYang H., Sun L., Wang Z., Li W., Liu G., Tang Y., ADMETopt: a web server for ADMET optimization in drug design via scaffold hopping. Journal of Chemical Information and Modeling, 2018, 58, 2051–2056. Abstract
AdmetSARYang H., Lou C., Sun L., Li J., Cai Y., Wang Z., Li W., Liu G., Tang Y., admetSAR 2.0: web-service for prediction and optimization of chemical ADMET properties. Bioinformatics, 2019, 35, 1067–1069. Abstract
ADVERPredIvanov S. M., Lagunin A. A., Rudik A. V., Filimonov D. A., Poroikov V. V., ADVERPred–web service for prediction of adverse effects of drugs. Journal of Chemical Information and Modeling, 2018, 58, 8–11. Abstract
Aggregator AdvisorIrwin J. J., Duan D., Torosyan H., Doak A. K., Ziebart K. T., Sterling T., Tumanian G., Shoichet B. K., An Aggregation Advisor for ligand discovery. Journal of Medicinal Chemistry, 2015, 58, 7076–7087. Abstract
AlkemioGijón-Correas J. A., Andrade-Navarro M. A., Fontaine J. F., Alkemio: association of chemicals with biomedical topics by text and data mining. Nucleic Acids Research, 2014, 42, W422–W429. Abstract
AlloFinderHuang M., Song K., Liu X., Lu S., Shen Q., Wang R., Gao J., Hong Y., Li Q., Ni D., Xu J., Chen G., Zhang J., AlloFinder: a strategy for allosteric modulator discovery and allosterome analyses. Nucleic Acids Research, 2018, 46, W451–W458. Abstract
ALOGPSTetko I. V., Bruneau P., Application of ALOGPS to predict 1-octanol/water distribution coefficients, logP, and logD, of AstraZeneca in-house database. J. Pharm. Sci., 2004, 93, 3103-3110. Abstract
AMMOS2Labbé C., Pencheva T., Jereva D., Desvillechabrol D., Becot J., Villoutreix B. O., Pajeva I., Miteva M. A., AMMOS2: a web server for protein–ligand–water complexes refinement via molecular mechanics. Nucleic Acids Research, 2017, 45, W350–W355. Abstract
AnchorQueryKoes D. R., Dömling A., Camacho C. J., AnchorQuery: Rapid online virtual screening for small-molecule protein–protein interaction inhibitors. Protein Science, 2018, 27, 229-232. Abstract
ASFPZhang X., Shen C., Guo X., Wang Z., Weng G., Ye Q., Wang G., He Q., Yang B., Cao D., Hou T., ASFP (Artificial Intelligence based Scoring Function Platform): a web server for the development of customized scoring functions. Journal of Cheminformatics, 2021, 13, Article No 6. Abstract
Atomic Charge CalculatorIonescu C.-M., Sehnal D., Falginella F. L., Pant P., Pravda L., Bouchal T., Svobodová Vařeková R., Geidl S., Koča J., Atomic charge calculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules. Journal of Cheminformatics, 2015, 7, Article No 50. Abstract
Atomic Charge Calculator IISchindler O., Raček T., Maršavelski A., Koča J., Berka K., Svobodová R., Optimized SQE atomic charges for peptides accessible via a web application. Journal of Cheminformatics, 13, Article No 45. Abstract
BATMAN-TCMLiu Z., Guo F., Wang Y., Li C., Zhang X., Li H., Diao L., Gu J., Wang W., Li D., He F., BATMAN-TCM: a Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine. Scientific Reports, 2016, 6, Article No 21146. Abstract
BayesilRavanbakhsh S., Liu P., Bjordahl T. C., Mandal R., Grant J. R., Wilson M., Eisner R., Sinelnikov I., Hu X., Luchinat C., Greiner R., Wishart D. S., Accurate, fully-automated NMR spectral profiling for metabolomics. PLoS ONE, 2015, 10, Article No e0124219. Abstract
BDPServerProvider: Centro Nacional de Biotecnologia, CSIC
BEEREYue Z., Willey C. D., Hjelmeland A. B., Chen J. Y., BEERE: a web server for biomedical entity expansion, ranking and explorations. Nucleic Acids Research, 2019, 47, W578–W586. Abstract
BiasNetSanchez J. E., KC G. B., Franco J., Allen W. J., Garcia J. D., Sirimulla S., BiasNet: a model to predict ligand bias toward GPCR signaling. J. Chem. Inf. Model., 2021, 61, 4190–4199. Abstract
BINANAYoung J., Garikipati N., Durrant J. D., BINANA 2: Characterizing receptor/ligand interactions in Python and JavaScript. Journal of Chemical Information and Modeling, 2022, 62, 753–760. Abstract
BiNChEMoreno P., Beisken S., Harsha B., Muthukrishnan V., Tudose I., Dekker A., Dornfeldt S., Taruttis F., Grosse I., Hastings J., Neumann S., Steinbeck C., BiNChE: A web tool and library for chemical enrichment analysis based on the ChEBI ontology. BMC Bioinformatics, 2015, 16, Article No 56. Abstract
Bioactivity-explorerLiang L., Ma C., Du T., Zhao Y., Zhao X., Liu M., Wang Z., Lin J., Bioactivity-explorer: a web application for interactive visualization and exploration of bioactivity data. Journal of Cheminformatics, 2019, 11, Article No 47. Abstract
BioMet ToolboxGarcia-Albornoz M., Thankaswamy-Kosalai S., Nilsson A., Väremo L., Nookaew I., Nielsen J., BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data. Nucleic Acids Research, 2014,42, W175–W181. Abstract
BioSilicoHou B. K., Kim J. S., Jun J. H., Lee D.-Y., Kim Y. W., Chae S., Roh M., In Y.-H., Lee S. Y., BioSilico: an integrated metabolic database system. Bioinformatics, 2004, 20, 3270-3272. Abstract
BioStatFlowProvider: INRA
Bio-TDSGnimpieba E. Z., VanDiermen M. S., Gustafson S. M., Conn B., Lushbough C. M., Bio-TDS: bioscience query tool discovery system. Nucleic Acids Research, 2017, 45, D1117–D1122. Abstract
BioTransformerDjoumbou Feunang Y., Fiamoncini J., de la Fuente A. G., Manach C., Greiner R., Wishart D. S., BioTransformer: a comprehensive computational tool for small molecule metabolism prediction and metabolite identification. Journal of Cheminformatics, 2019, 11, Article No 2. Abstract
BioTriangleDong J., Yao Z.-J., Wen M., Zhu M.-F., Wang N.-N., Miao H.-Y., Lu A.-P., Zeng W.-B., Cao D.-S., BioTriangle: a web‑accessible platform for generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions. Journal of Cheminformatics, 2016, 8, Article No 34. Abstract
BitterPredictDagan-Wiener A., Nissim I., Ben Abu N., Borgonovo G., Bassoli A., Niv M. Y., Bitter or not? BitterPredict, a tool for predicting taste from chemical structure. Scientific Reports, 2017, 7, Article No 12074. Abstract
BitterXHuang W., Shen Q., Su X., Ji M., Liu X., Chen Y., Lu S., Zhuang H., Zhang J., BitterX: a tool for understanding bitter taste in humans. Scientific Reports, 2016, 6, Article No 23450. Abstract
BoBERLešnik S., Škrlj B., Eržen N., Bren U., Gobec S., Konc J., Janežič D., BoBER: web interface to the base of bioisosterically exchangeable replacements. Journal of Cheminformatics, 2017, 9, Article No 62. Abstract
CACTUS websiteSitzmann M., Filippov I.V., Nicklaus M.C., Internet resources integrating many small molecular databases. SAR QSAR in Environmental Research, 2008, 19, 1-9. Abstract
CarcinoPred-ELZhang L., Ai H., Chen W., Yin Z., Hu H., Zhu J., Zhao J., Zhao Q., Liu H., CarcinoPred-EL: Novel models for predicting the carcinogenicity of chemicals using molecular fingerprints and ensemble learning methods. Scientific Reports, 2017, 7, Article No 2118. Abstract
CB-DockLiu Y., Grimm M., Dai W., Hou M., Xiao Z.-X., Cao Y., CB-Dock: a web server for cavity detection-guided protein–ligand blind docking. Acta Pharmacologica Sinica, 2020, 41, 138–144. Abstract
CDPsGonzález-Medina M., Prieto-Martínez F. D., Owen J. R., Medina-Franco J. L., 2016, Consensus Diversity Plots: a global diversity analysis of chemical libraries. Journal of Cheminformatics, 2016, 8, Article No 63. Abstract
CDRUGLi G.-H., Huang J.-F., CDRUG: a web server for predicting anticancer activity of chemical compounds.  Bioinformatics, 2012, 28, 3334-3335. Abstract
CFM-IDAllen F., Pon A., Wilson M., Greiner R., Wishart D., CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra. Nucleic Acids Research, 2014, 42, W94–W99. Abstract
ChAIPredSharma N., Patiyal S., Dhall A., Devi N. L., Raghava G. P. S., ChAlPred: A web server for prediction of allergenicity of chemical compounds. Computers in Biology and Medicine, 2021, 136, Article No 104746. Abstract
CheckMyBlobBrzezinski D., Porebski P. J., Kowiel M., Macnar J. M., Minor W., Recognizing and validating ligands with CheckMyBlob. Nucleic Acids Research, 2021, 49, W86–W92. Abstract
ChemBCPPDong J., Wang N.-N., Liu K.-Y., Zhu M.-F., Yun Y.-H., Zeng W.-B., Chen A. F., Cao D.-S., ChemBCPP: A freely available web server for calculating commonly used physicochemical properties. Chemometrics and Intelligent Laboratory Systems, 2017, 171, 65–73. Abstract
ChemBioNavigatorStierand K., Harder T., Marek T., Hilbig M., Lemmen C., Rarey M., The internet as scientific knowledge base: Navigating the chem-bio space. Molecular Informatics, 2012, 31, 543-546. Abstract
ChemBioServerAthanasiadis E., Cournia Z., Spyrou G., ChemBioServer: a web-based pipeline for filtering, clustering and visualization of chemical compounds used in drug discovery. Bioinformatics, 2012, 28, 3002-3003. Abstract
ChEMBL BrowserReymond J.-L., The chemical space project. Accounts of Chemical Research, 2015, 48, 722–730. Abstract
ChemCalcPatiny L., Borel A., ChemCalc: A building block for tomorrow’s chemical infrastructure. Journal of Chemical Information and Modeling, 2013, 53, 1223–1228. Abstract
ChemDesDong J., Cao D.-S., Miao H.-Y., Liu S., Deng B.-C., Yun Y.-H., Wang N.-N., Lu A.-P., Zeng W.-B., Chen A. F., ChemDes: an integrated web‑based platform for molecular descriptor and fingerprint computation. Journal of Cheminformatics, 2015, 7, 60. Abstract
ChemFluoYang Z.-Y., Dong J., Yang Z.-J., Yin M., Jiang H.-L., Lu A.-P., Chen X., Hou T.-J., Cao D.-S., ChemFLuo: a web-server for structure analysis and identification of fluorescent compounds. Briefings in Bioinformatics, 2021, 22, Article No bbaa282. Abstract
ChemGeneratorYang J., Hou L., Liu K.-M., He W.-B, Cai Y., Yang F.-Q., Hu Y.-J., ChemGenerator: a web server for generating potential ligands for specific targets. Briefings in Bioinformatics, 2021, 22, Article No bbaa407. Abstract
Chemical Activity PredictorProvider: National Institutes of Health
Chemical Identifier ResolverMuresan S., Sitzmann M., Southan C., Mapping between databases of compounds and protein targets. Methods in Molecular Biology, 2012, 910, 145-164. Abstract
Chemical Structure LookupSitzmann M., Filippov I.V., Nicklaus M.C., Internet resources integrating many small molecular databases. SAR QSAR in Environmental Research, 2008, 19, 1-9. Abstract
Chemicalize.orgSouthan C., Stracz A., Extracting and connecting chemical structures from text sources using chemicalize.org. Journal of Cheminformatics, 2013, 5, Article No 20. Abstract
ChemicalToolboxBray S. A., Lucas X., Kumar A., Grüning B. A., The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform. Journal of Cheminformatics, 2020, 12, Article No 40. Abstract
Chemical Translation ServiceWohlgemuth G., Haldiya P. K., Willighagen E., Kind T., Fiehn O., The Chemical Translation Service – a web-based tool to improve standardization of metabolomic reports. Bioinformatics, 2010, 26, 2647–2648. Abstract
ChemMapperGong J., Cai C., Liu X., Ku X., Jiang H., Gao D., Li H., ChemMapper: a versatile web server for exploring pharmacology and chemical structure association based on molecular 3D similarity method. Bioinformatics, 2013, 29, 1827-1829. Abstract
ChemMapsBorrel A., Kleinstreuer N. C., Fourches D., Exploring drug space with ChemMaps.com. Bioinformatics, 2018, 34, 3773–3775. Abstract
ChemMineBackman T. W. H., Cao Y., Girke T., ChemMine tools: an online service for analyzing and clustering small molecules. Nucleic Acids Research, 2011, 39, W486–W491. Abstract
ChemotextCapuzzi S. J., Thornton T. E., Liu K., Baker N., Lam W. I., O’Banion C. P., Muratov E. N., Pozefsky D., Tropsha A., Chemotext: a publicly available web server for mining drug–target–disease relationships in PubMed. Journal of Chemical Information and Modeling, 2018, 58, 212–218. Abstract
ChemSARDong J., Yao Z.-J., Zhu M.-F., Wang N.-N., Lu B., Chen A. F., Lu A.-P., Miao H., Zeng W.-B., Cao D.-S., ChemSAR: an online pipelining platform for molecular SAR modeling. Journal of Cheminformatics, 2017, 9, Article No 27. Abstract
CILGrüning B. A., Senger C., Erxleben A., Flemming S., Günther S., Compounds In Literature (CIL): screening for compounds and relatives in PubMed. Bioinformatics, 2011, 27, 1341–1342. Abstract
Click2DrugProvider: Swiss Institute of Bioinformatics
ClusProPorter K. A., Xia B., Beglov D., Bohnuud T., Alam N., Schueler-Furman O., Kozakov D., ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT. Bioinformatics, 2017, 33, 3299–3301. Abstract
ClustVisMetsalu T., Vilo J., ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap. Nucleic Acids Research, 2015, 43, W566–W570. Abstract
CMCLiu L., Tsompana M., Wang Y., Wu D., Zhu L., Zhu R., Connection Map for Compounds (CMC): a server for combinatorial drug toxicity and efficacy analysis. Journal of Chemical Information and Modeling, 2016, 56, 1615–1621. Abstract
COACH-DWu Q., Peng Z., Zhang Y., Yang J., COACH-D: improved protein–ligand binding sites prediction with refined ligand-binding poses through molecular docking. Nucleic Acids Research, 2018, 46, W438–W442. Abstract
CollectorLópez-Massaguer O., Sanz F., Pastor M., An automated tool for obtaining QSAR-ready series of compounds using semantic web technologies. Bioinformatics, 2018, 34, 131–133. Abstract
ConvertProvider: University of New Mexico
COPICATSakakibara Y., Hachiya T., Uchida M., Nagamine N., Sugawara Y., Yokota M., Nakamura M., Popendorf K., Komori T., Sato K., COPICAT: a software system for predicting interactions between proteins and chemical compounds. Bioinformatics, 2012, 28, 745-746. Abstract
COSMOSSadowski P., Baldi P., Small-molecule 3D structure prediction using open crystallography data. Journal of Chemical Information and Modeling, 2013, 53, 3127–3130. Abstract
CovalentDock CloudOuyang X. Zhou S., Ge Z., Li R., Kwoh C. K., CovalentDock Cloud: a web server for automated covalent docking. Nucleic Acids Research, 2013, 41, W329-W332. Abstract
CRDD websiteProvider: IMTECH/CSIR
CRDSLee A., Kim D., CRDS: consensus reverse docking system for target fishing. Bioinformatics, 2020, 36, 959–960. Abstract
CSI:FingerIDDührkop K., Shen H., Meusel M., Rousu J., Böcker S., Searching molecular structure databases with tandem mass spectra using CSI:FingerID. Proceedings of the National Academy of Sciences of the United States of America, 2015, 112, 12580–12585. Abstract
CSM-ligPires D. E. V., Ascher D. B., CSM-lig: a web server for assessing and comparing protein–small molecule affinities. Nucleic Acids Research, 2016, 44, W557–W561. Abstract
CSNAPLo Y.-C., Senese S., Li C.-M., Hu Q., Huang Y., Damoiseaux R., Torres J. Z., Large-scale chemical similarity networks for target profiling of compounds identified in cell-based chemical screens. PLoS Computational Biology, 2015, 11, Article No e1004153. Abstract
C-SPADERavikumar B., Alam Z., Peddinti G., Aittokallio T., C-SPADE: a web-tool for interactive analysis and visualization of drug screening experiments through compound-specific bioactivity dendrograms. Nucleic Acids Research, 2017, 45, W495–W500. Abstract
CycloPsDuffy F. J., Verniere M., Devocelle M., Bernard E., Shields D. C., Chubb A. J., CycloPs: generating virtual libraries of cyclized and constrained peptides including nonnatural amino acids. Journal of Chemical Information and Modeling, 2011, 51, 829-836. Abstract
DASPfindBa‑alawi W., Soufan O., Essack M., Kalnis P., Bajic V. B., DASPfind: new efficient method to predict drug–target interactions. Journal of Cheminformatics, 2016, 8, Article No 15. Abstract
DECIMERRajan K., Brinkhaus H. O., Sorokina M., Zielesny A., Steinbeck C., DECIMER‑Segmentation: Automated extraction of chemical structure depictions from scientific literature. Journal of Cheminformatics, 2021, 13, Article No 20. Abstract
DeepFragGreen H., Durrant J. D., DeepFrag: an open-source browser app for deep-learning lead optimization. Journal of Chemical Information and Modeling, 2021, 61, 2523-2529. Abstract
DeepScreeningLiu Z., Du J., Fang J., Yin Y., Xu G., Xie L., 2019, DeepScreening: a deep learning-based screening web server for accelerating drug discovery. Database, Article No baz104. Abstract
DeepSynergyPreuer K., Lewis R. P. I., Hochreiter S., Bender A., Bulusu K. C., Klambauer G., DeepSynergy: predicting anti-cancer drug synergy with Deep Learning. Bioinformatics, 2018, 34, 1538–1546. Abstract
Dendrimer BuilderProvider: University of Bern
DIGREMZhang M., Lee S., Yao B., Xiao G., Xu L., Xie Y., DIGREM: an integrated web-based platform for detecting effective multi-drug combinations. Bioinformatics, 2019, 35, 1792–1794. Abstract
DINIESYamanishi Y., Kotera M., Moriya Y., Sawada R., Kanehisa M., Goto S., DINIES: drug–target interaction network inference engine based on supervised analysis. Nucleic Acids Research, 2014, 42, W39–W45. Abstract
DockThorSantos K. B., Guedes I. A., Karl A. L. M., Dardenne L. E., Highly flexible ligand docking: benchmarking of the DockThor program on the LEADS-PEP protein–peptide data set. Journal of Chemical Information and Modeling, 2020, 60, 667-683. Abstract
D-Peptide BuilderDíaz-Eufracio B. I., Palomino-Hernández O., Arredondo-Sánchez A., Medina-Franco J. L., D-Peptide Builder: a web service to enumerate, analyze, and visualize the chemical space of combinatorial peptide libraries. Molecular Informatics, 2020, 39, Article No 2000035. Abstract
DPubChemSoufan O., Ba-alawi W., Magana-Mora A., Essack M., Bajic V. B., DPubChem: a web tool for QSAR modeling and high-throughput virtual screening. Scientific Reports, 2018, 8, Article No 9110. Abstract
DrawGlycan-SFNGCheng K., Zhou Y., Neelamegham S., DrawGlycan-SNFG: a robust tool to render glycans and glycopeptides with fragmentation information. Glycobiology, 2017, 27, 200–205. Abstract
DrugBank MQN BrowserReymond J.-L., The chemical space project. Accounts of Chemical Research, 2015, 48, 722–730. Abstract
DrugBank SMIfp BrowserReymond J.-L., The chemical space project. Accounts of Chemical Research, 2015, 48, 722–730. Abstract
DrugCombZheng S., Aldahdooh J., Shadbahr T., Wang Y., Aldahdooh D., Bao J., Wang W., Tang J., DrugComb update: a more comprehensive drug sensitivity data repository and analysis portal. Nucleic Acids Research, 2021, 49, W174–W184. Abstract
DrugE-RankYuan Q., Gao J., Wu D., Zhang S., Mamitsuka H., Zhu S., DrugE-Rank: improving drug–target interaction prediction of new candidate drugs or targets by ensemble learning to rank. Bioinformatics, 2016, 32, i18–i27. Abstract
DrugMintDhanda S. K., Singla D., Mondal A. K., Raghava G. P. S., DrugMint: a webserver for predicting and designing of drug-like molecules. Biology Direct, 2013, 8, Article No 28. Abstract
DrugmonizomeKropiwnicki E., Evangelista J. E., Stein D. J., Clarke D. J. B., Lachmann A., Kuleshov M. V., Jeon M., Jagodnik K. M., Ma’ayan A., Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning. Database, 2021, Article No baab017. Abstract
DrugQuestPapanikolaou N., Pavlopoulos G. A., Theodosiou T., Vizirianakis I. S., Iliopoulos I., DrugQuest – a text mining workflow for drug association discovery. BMC Bioinformatics, 2016, 17 (Suppl 5), Article No 182. Abstract
Drug ReposER
Ab Ghani N. S., Ramlan E. I., Firdaus-Raih M., Drug ReposER: a web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning. Nucleic Acids Research, 2019, 47, W350–W356. Abstract
Drug Target ProfilerTanoli Z., Alam Z., Ianevski A., Wennerberg K., Vähä-Koskela M., Aittokallio T., Interactive visual analysis of drug–target interaction networks using Drug Target Profiler, with applications to precision medicine and drug repurposing. Briefings in Bioinformatics, 2020, 21, 211–220. Abstract
EBI Search EnginePark Y. M., Squizzato S., Buso N., Gur T., Lopez R., The EBI search engine: EBI search as a service-making biological data accessible for all. Nucleic Acids Research, 2017, 45, W545–W549. Abstract
EDockZhang W., E. W., Yin M., Zhang Y., EDock: blind protein–ligand docking by replica‑exchange Monte Carlo simulation. Journal of Cheminformatics, 2020, 12, Article No 37. Abstract
eMolToxJi C., Svensson F., Zoufir A., Bender A., eMolTox: prediction of molecular toxicity with confidence. Bioinformatics, 2018, 34, 2508–2509. Abstract
Epigenetic Target ProfilerSánchez-Cruz N., Medina-Franco J. L., Epigenetic Target Profiler: a web server to predict epigenetic targets of small molecules. Journal of Chemical Information and Modeling, 2021, 61, 1550–1554. Abstract
ePlattonDu Y., Shi T., Ligand cluster-based protein network and ePlatton, a multi-target ligand finder. Journal of Cheminformatics, 2016, 8, Article No 23. Abstract
E-zymeYamanishi Y., Hattori M., Kotera M., Goto S., Kanehisa M., E-zyme: Predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs. Bioinformatics, 2009, 25, i179-i186. Abstract
FAERUNProbst D., Reymond J.-L., FUn: A framework for interactive visualizations of large, high-dimensional datasets on the web. Bioinformatics, 2018, 34, 1433-1435. Abstract
FAF-Drugs4Lagorce D., Bouslama L., Becot J., Miteva M. A., Villoutreix B. O., FAF-Drugs4: free ADME-tox filtering computations for chemical biology and early stages drug discovery. Bioinformatics, 2017, 22, 3658–3660. Abstract
FAME 3Šícho M., Stork C., Mazzolari A., de Bruyn Kops C., Pedretti A., Testa B., Vistoli G., Svozil D., Kirchmair J., FAME 3: Predicting the sites of metabolism in synthetic compounds and natural products for phase 1 and phase 2 metabolic enzymes. Journal of Chemical Information and Modeling, 2019, 59, 3400-3412. Abstract
FEPrepareZavitsanou S., Tsengenes A., Papadourakis M., Amendola G., Chatzigoulas A., Dellis D., Cosconati S., Cournia Z., FEPrepare: a web-based tool for automating the setup of relative binding free energy calculations. Journal of Chemical Information and Modeling, 2021, 61, 4131-4138. Abstract
FINDSITEcomb2.0Zhou H., Cao H., Skolnick J., FINDSITEcomb2.0: A new approach for virtual ligand screening of proteins and virtual target screening of biomolecules. Journal of Chemical Information and Modeling, 2018, 58, 2343–2354. Abstract
FingerIDDührkop K., Shen H., Meusel M., Rousu J., Böcker S., Searching molecular structure databases with tandem mass spectra using CSI:FingerID. Proceedings of the National Academy of Sciences of the United States of America, 2015, 112, 12580–12585. Abstract
FitDockYang X., Liu Y., Gan J., Xiao Z.-X., Cao Y., FitDock: protein–ligand docking by template fitting. Briefings in Bioinformatics, 2022, 23, Article No bbac087. Abstract
FMMChou C. H., Chang W. C., Chiu C. M., Huang C. C., Huang H. D., FMM: a web server for metabolic pathway reconstruction and comparative analysis. Nucleic Acids Research, 2009, 37, W129-W134. Abstract
foodMASSTWest K. A., Schmid R., Gauglitz J. M., Wang M., Dorrestein P. C., foodMASST a mass spectrometry search tool for foods and beverages. Science of Food, 2022, 6, Article No 22. Abstract
Fragrance BrowserRuddigkeit L., Awale M., Reymond J.-L., Expanding the fragrance chemical space for virtual screening. Journal of Cheminformatics, 2014, 6, Article No 27. Abstract
FragRepShan J., Pan X., Wang X., Xiao X., Ji C., FragRep: a web server for structure-based drug design by fragment replacement. Journal of Chemical Information and Modeling, 2020, 60, 5900-5906. Abstract
GalahadLaenen G., Ardeshirdavani A., Moreau Y., Thorrez L., Galahad: a web server for drug effect analysis from gene expression. Nucleic Acids Research, 2015, 43, W208-W212. Abstract
Galaxy7TMLee G. R., Seok C., Galaxy7TM: flexible GPCR–ligand docking by structure refinement. Nucleic Acids Research, 2016, 44, W502–W506. Abstract
GalaxySagittariusYang J., Kwon S., Bae S.-H., Park K. M., Yoon C., Lee J.-H., Seok C., GalaxySagittarius: structure- and similarity-based prediction of protein targets for druglike compounds. Journal of Chemical Information and Modeling, 2020, 60, 3246–3254. Abstract
GDACaroli J., Sorrentino G., Forcato M., Del Sal G., Bicciato S., GDA, a web-based tool for Genomics and Drugs integrated analysis. Nucleic Acids Research, 2018, 46, W148–W156. Abstract
GIANTKasahara K., Kinoshita K., GIANT: pattern analysis of molecular interactions in 3D structures of protein–small ligand complexes. BMC Bioinformatics, 15, Article No 12. Abstract
Glycam WebProvider: University of Georgia
GlycanBuilderDamerell D., Ceroni A., Maass K., Ranzinger R., Dell A., Haslam S. M., 2012, The GlycanBuilder and GlycoWorkbench glycoinformatics tools: updates and new developments. Biological Chemistry, 2012, 393, 1357-1362. Abstract Tsuchiya S., Aoki N. P., Shinmachi D., Matsubara M., Yamada I., Aoki-Kinoshita K. F., Narimatsu H., Implementation of GlycanBuilder to draw a wide variety of ambiguous glycans. Carbohydrate Research, 2017, 445, 104-116. Abstract
GlycoDigestGotz L., Abrahams J. L., Mariethoz J., Rudd P. M., Karlsson N. G., Packer N. H., Campbell M. P., Lisacek F., GlycoDigest: a tool for the targeted use of exoglycosidase digestions in glycan structure determination. Bioinformatics, 2014, 30, 3131-3133. Abstract
GlycoFragmentsLohmann K.K., von der Lieth C.-W., GlycoFragment and GlycoSearchMS: web tools to support the interpretation of mass spectra of complex carbohydrates. Nucleic Acids Research, 2004, W261–W266. Abstract
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KiDoQGarg A., Tewari R., Raghava G. P. S., KiDoQ: using docking based energy scores to develop ligand based model for predicting antibacterials. BMC Bioinformatics, 2010, 11, Article No 125. Abstract
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SwissParamZoete V., Cuendet M. A., Grosdidier A., Michielin O., SwissParam, a fast force field generation tool for small organic molecules. Journal of Computational Chemistry, 2011, 32, 2359-2368. Abstract
SwissSimilarityZoete V., Daina A., Bovigny C., Michielin O., SwissSimilarity: a web tool for low to ultra high throughput ligand-based virtual screening. Journal of Chemical Information and Modeling, 2016, 56, 1399–1404. Abstract
SwissTargetPredictionDaina A., Michielin O., Zoete V., SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules. Nucleic Acids Research, 2019, 47, W357–W364. Abstract
SynergyFinderIanevski A., Giri A. K., Aittokallio T., SynergyFinder 2.0: visual analytics of multi-drug combination synergies. Nucleic Acids Research, 2020, 48, W488-W493. Abstract
systemsDockHsin K.-Y., Matsuoka Y., Asai Y., Kamiyoshi K., Watanabe T., Kawaoka Y., Kitano H., systemsDock: a web server for network pharmacology-based prediction and analysis. Nucleic Acids Research, 2016, 44, W507–W513. Abstract
TCMAnalyzerLiu Z., Du J., Yan X., Zhong J., Cui L., Lin J., Zeng L., Ding P., Chen P., Zhou X., Zhou H., Gu Q., Xu J., TCMAnalyzer: a chemo- and bioinformatics web service for analyzing traditional Chinese medicine. Journal of Chemical Information and Modeling, 2018, 58, 550–555. Abstract
TNFPubChemMelagraki G., Ntougkos E., Rinotas V., Papaneophytou C., Leonis G., Mavromoustakos T., Kontopidis G., Douni E., Afantitis A., Kollias G., Cheminformatics-aided discovery of small-molecule Protein-Protein Interaction (PPI) dual inhibitors of Tumor Necrosis Factor (TNF) and Receptor Activator of NF-κB ligand (RANKL). PLoS Computational Biology, 2017, 13, Article No e1005372. Abstract
ToxAnalyzerRodrigues D. R., Batista Mariano D. C., Silva Santos L. H., Tagliati C. A., ToxAnalyzer: A user-friendly web tool for interactive data analysis and visualization of chemical compounds from the Comparative Toxicogenomics Database (CTD)™. Computational Toxicology, 2021, 19, Article No 100170. Abstract
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ToxiPredMishra N. K., Singla D., Agarwal S., Open Source Drug Discovery Consortium, Raghava G. P. S., ToxiPred: a server for prediction of aqueous toxicity of small chemical molecules in T. pyriformis. Journal of Translational Toxicology, 2014, 1, 21-27. Abstract
University of Berne websiteReymond J.-L., The chemical space project. Accounts of Chemical Research, 2015, 48, 722–730. Abstract
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VEGA On-linePedretti V., Villa L., Vistoli G., VEGA – An open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming. Journal of Computer-Aided Molecular Design, 2004, 18, 167–173. Abstract
VennyAuthor: Juan Carlos Oliveros; Provider: Centro Nacional de Biotecnología, (CNB-CSIC)
Virtual LogPGaillard P., Carrupt P. A., Testa B., Boudon A., Molecular lipophilicity potential, a tool in 3D QSAR: method and applications. Journal of Computer-Aided Molecular Design, 1994, 8, 83-96. Abstract
VirtualTasteFritz F., Preissner R., Banerjee P., VirtualTaste: a web server for the prediction of organoleptic properties of chemical compounds. Nucleic Acids Research, 2021, 49, W679–W684. Abstract
vsFiltGushchina I. V., Polenova A. M., Suplatov D. A., Švedas V. K., Nilov D. K., vsFilt: a tool to improve virtual screening by structural filtration of docking poses. Journal of Chemical Information and Modeling, 2020, 60, 3692–3696. Abstract
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WebinaKochnev Y., Hellemann E., Cassidy K. C., Durrant J. D., Webina: an open-source library and web app that runs AutoDock Vina entirely in the web browser. Bioinformatics, 2020, 36, 4513–4515. Abstract
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Wikipedia Chemical Structure ExplorerErtl P., Patiny L., Sander T., Rufener C., Zasso M., Wikipedia Chemical Structure Explorer: substructure and similarity searching of molecules from Wikipedia. Journal of Cheminformatics, 2015, 7, Article No 10. Abstract
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XenoNetFlynn N. R., Le Dang N., Ward M. D., Swamidass S. J., XenoNet: inference and likelihood of intermediate metabolite formation. Journal of Chemical Information and Modeling, 2020, 60, 3431–3449. Abstract
ZINC BrowserAwale M., Reymond J.-L., A multi-fingerprint browser for the ZINC database. Nucleic Acids Research, 2014, 42, W234–W239. Abstract
ZINC ExpressBobrowski T. M., Korn D. R., Muratov E. N., Tropsha A., ZINC Express: a virtual assistant for purchasing compounds annotated in the ZINC database. Journal of Chemical Information and Modeling, 2021, 61, 1033–1036. Abstract