Programs
| 3DMolMS | Hong Y., Li S., Welch C. J., Tichy S., Ye Y., Tang H., 3DMolMS: prediction of tandem mass spectra from 3D molecular conformations. Bioinformatics, 2023, 39, Article No btad354. Abstract |
| 4-way Venn Diagram Generator | Author: Chris Seidel |
| ACFIS | Shi X.-X., Wang Z.-Z., Wang F., Hao G.-F., Yang G.-F., 2023, ACFIS 2.0: an improved web-server for fragment-based drug discovery via a dynamic screening strategy. Nucleic Acids Research, 2023, 51, W25–W32. Abstract |
| ACID | Wang 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 |
| ACPYPE | Kagami L., Wilter A., Diaz A., Vranken V., The ACPYPE web server for small-molecule MD topology generation. Bioinformatics, 2023, 39, Article No btad350. Abstract |
| Activity Landscape Plotter | González-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 SARfari | Davies 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 |
| ADMETlab | Dong 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 2.0 | Xiong 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 |
| ADMETopt | Yang 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 |
| AdmetSAR | Yang 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 |
| ADVERPred | Ivanov 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 Advisor | Irwin 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 |
| Alkemio | Gijón-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 |
| AlloFinder | Huang 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 |
| ALOGPS | Tetko 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 |
| AMMOS2 | Labbé 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 |
| AnchorQuery | Koes 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 |
| antiSMASH | Blin K., Shaw S., Augustijn H. E., Reitz Z. L., Biermann F., Alanjary M., Fetter A., Terlouw B. R., Metcalf W. W., Helfrich E. J. N., van Wezel G. P., Medema M. H., Weber T., antiSMASH 7.0: new and impr o ved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Research, 2023, 51, W46–W50. Abstract |
| ASFP | Zhang 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 Calculator | Ionescu 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 II | Schindler 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-TCM | Kong X., Liu C., Zhang Z., Cheng M., Mei Z., Li X., Liu P., Diao L., Ma Y., Jiang P., Kong X., Nie S., Guo Y., Wang Z., Zhang X., Wang Y., Tang L., Guo S., Liu Z., Li D., BATMAN-TCM 2.0: an enhanced integrative database for known and predicted interactions between traditional Chinese medicine ingredients and target proteins. Nucleic Acids Research, 2024, 52, D1110–D1120. Abstract |
| Bayesil | Ravanbakhsh 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 |
| BDPServer | Provider: Centro Nacional de Biotecnologia, CSIC |
| BEERE | Yue 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 |
| BiasNet | Sanchez 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 |
| BINANA | Young 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 |
| BiNChE | Moreno 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-explorer | Liang 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 Toolbox | Garcia-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 |
| BioSilico | Hou 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 |
| BioStatFlow | Provider: INRA |
| Bio-TDS | Gnimpieba 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 |
| BioTransformer | Wishart D. S., Tian S., Allen D., Oler E., Peters H., Lui V. W., Gautam V., Djoumbou-Feunang Y., Greiner R., Metz T. O., BioTransformer 3.0–a web server for accurately predicting metabolic transformation products. Nucleic Acids Research, 2022, 50, W115–W123. Abstract |
| BioTriangle | Dong 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 |
| BitterPredict | Dagan-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 |
| BitterSweet Predict | Tuwani R., Wadhwa S., Bagler G., BitterSweet: building machine learning models for predicting the bitter and sweet taste of small molecules. Scientific Reports, 2019, 9, Article No 7155. Abstract |
| BitterX | Huang 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 |
| BMaps | Bryan D. R., Kulp J. L. Jr., Mahapatra M. K., Bryan R. L., Viswanathan U., Carlisle M. N., Kim S., Schutte W. D., Clarke K. V., Doan T. T., Kulp J. L. III, BMaps: A web application for fragment-based drug design and compound binding evaluation. Journal of Chemical Information and Modeling, 2023, 63, 4229–4236. Abstract |
| BoBER | Lešnik 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 |
| Breeze | Potdar S., Ianevski F., Ianevski A.,Tanoli Z., Wennerberg W., Seashore-Ludlow B., Kallioniemi O., Östling P., Aittokallio T., Saarela J., Breeze 2.0: an interactive web-tool for visual analysis and comparison of drug response data. Nucleic Acids Research, 2023, 51, W57–W61. Abstract |
| CACTUS website | Sitzmann M., Filippov I.V., Nicklaus M.C., Internet resources integrating many small molecular databases. SAR QSAR in Environmental Research, 2008, 19, 1-9. Abstract |
| CADDIE | Hartung M., Anastasi E., Mamdouh Z. M., Nogales C., Schmidt H. H. H. W., Baumbach J., Zolotareva O., List M., Cancer driver drug interaction explorer. Nucleic Acids Research, 2022, 50, W138–W144. Abstract |
| CarcinoPred-EL | Zhang 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 |
| cardioToxCSM | Iftkhar S., de Sá A. G. C., Velloso J. P. L., Aljarf R., Pires D. E. V., Ascher D. B., cardioToxCSM: A web server for predicting cardiotoxicity of small molecules. Journal of Chemical Information and Modeling, 2022, 62, 4827-4836. Abstract |
| CAVE | Mao Z., Yuan Q., Li H., Zhang Y., Huang Y., Yang C., Wang R., Yang Y., Wu Y., Yang S., Liao X., Ma H., CAVE: a cloud-based platform for analysis and visualization of metabolic pathways. Nucleic Acids Research, 2023, 51, W70–W77. Abstract |
| CB-Dock | Liu 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 |
| CB-Dock2 | Liu Y., Yang X., Gan J., Chen S., Xiao Z.-X., Cao Y., CB-Dock2: improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting. Nucleic Acids Research, 2022, 50, W159–W164. Abstract |
| CDPs | González-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 |
| CDRUG | Li G.-H., Huang J.-F., CDRUG: a web server for predicting anticancer activity of chemical compounds. Bioinformatics, 2012, 28, 3334-3335. Abstract |
| CFM-ID | Wang F., Allen D., Tian S., Oler E., Gautam V., Greiner R., Metz T. O., Wishart D. S., CFM-ID 4.0 – a web server for accurate MS-based metabolite identification. Nucleic Acids Research, 2022, 50, W165–W174. Abstract |
| ChAIPred | Sharma 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 |
| CheckMyBlob | Brzezinski 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 |
| ChemBCPP | Dong 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 |
| ChemBioNavigator | Stierand 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 |
| ChemBioServer | Athanasiadis 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 Browser | Reymond J.-L., The chemical space project. Accounts of Chemical Research, 2015, 48, 722–730. Abstract |
| ChemCalc | Patiny L., Borel A., ChemCalc: A building block for tomorrow’s chemical infrastructure. Journal of Chemical Information and Modeling, 2013, 53, 1223–1228. Abstract |
| ChemCompute | Provider: Sonoma State University |
| ChemDes | Dong 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 |
| ChemFluo | Yang 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 |
| ChemGenerator | Yang 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 Predictor | Provider: National Institutes of Health |
| Chemical Identifier Resolver | Muresan S., Sitzmann M., Southan C., Mapping between databases of compounds and protein targets. Methods in Molecular Biology, 2012, 910, 145-164. Abstract |
| Chemical Structure Lookup | Sitzmann 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.org | Southan C., Stracz A., Extracting and connecting chemical structures from text sources using chemicalize.org. Journal of Cheminformatics, 2013, 5, Article No 20. Abstract |
| ChemicalToolbox | Bray 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 Service | Wohlgemuth 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 |
| ChemMapper | Gong 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 |
| ChemMaps | Borrel A., Conway M., Nolte S. Z., Unnikrishnan A., Schmitt C. P., Kleinstreuer N. C., ChemMaps.com v2.0: exploring the environmental chemical universe. Nucleic Acids Research, 2023, 51, W78–W82. Abstract |
| ChemMine | Backman 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 |
| ChemMORT | Yi J.-C., Yang Z.-Y., Zhao W.-T., Yang Z.-J., Zhang X.-C., Wu C.-K., Lu A.-P., Cao D.-S., ChemMORT: an automatic ADMET optimization platform using deep learning and multi-objective particle swarm optimization. Briefings in Bioinformatics, 2024, 25, Article No bbae008. Abstract |
| Chemotext | Capuzzi 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 |
| ChemSAR | Dong 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 |
| CIL | Grüning 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 |
| Click2Drug | Provider: Swiss Institute of Bioinformatics |
| ClusPro | Porter 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 |
| ClustVis | Metsalu 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 |
| CMC | Liu 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 | Yang J., Roy A., Zhang Y., Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. Bioinformatics, 2013, 29, 2588-2595. Abstract |
| COACH-D | Wu 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 |
| CODD-Pred | Yin X., Wang X., Li Y., Wang J., Wang Y., Deng Y., Hou T., Liu H., Luo P., Yao X., CODD-Pred: A web server for efficient target identification and bioactivity prediction of small molecules. Journal of Chemical Information and Modeling, 2023, 63, 6169–6176. Abstract |
| Collector | López-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 |
| Convert | Provider: University of New Mexico |
| COPICAT | Sakakibara 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 |
| COSMOS | Sadowski P., Baldi P., Small-molecule 3D structure prediction using open crystallography data. Journal of Chemical Information and Modeling, 2013, 53, 3127–3130. Abstract |
| CovalentDock Cloud | Ouyang 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 |
| CPRiL | Qaseem A., Günther S., CPRiL: compound–protein relationships in literature. Bioinformatics, 2022, 38, 4452–4453. Abstract |
| CRDD website | Provider: IMTECH/CSIR |
| CRDS | Lee A., Kim D., CRDS: consensus reverse docking system for target fishing. Bioinformatics, 2020, 36, 959–960. Abstract |
| CSI:FingerID | Dührkop 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-lig | Pires 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 |
| CSNAP | Lo 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-SPADE | Ravikumar 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 |
| CycloPs | Duffy 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 |
| DASPfind | Ba‑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 |
| dbCAN3 | Zheng J., Ge Q., Yan Y., Zhang X., Huang L., Yin Y., dbCAN3: automated carbohydrate-active enzyme and substrate annotation. Nucleic Acids Research, 2023, 51, W115–W121. Abstract |
| DECIMER | Rajan 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 |
| DeepAR | Schaduangrat N., Anuwongcharoen N., Charoenkwan P., Shoombuatong W., DeepAR: a novel deep learning‑based hybrid framework for the interpretable prediction of androgen receptor antagonists. Journal of Cheminformatics, 2023, 15, Article No 50. Abstract |
| DeepFrag | Green 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 |
| DeepScreening | Liu 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 |
| DeepSynergy | Preuer 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 Builder | Provider: University of Bern |
| DIGREM | Zhang 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 |
| DINIES | Yamanishi 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 |
| DockThor | Santos 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 Builder | Díaz-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 |
| DPubChem | Soufan 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-SFNG | Cheng 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 Browser | Reymond J.-L., The chemical space project. Accounts of Chemical Research, 2015, 48, 722–730. Abstract |
| DrugBank SMIfp Browser | Reymond J.-L., The chemical space project. Accounts of Chemical Research, 2015, 48, 722–730. Abstract |
| DrugComb | Zheng 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-Rank | Yuan 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 |
| DrugMint | Dhanda 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 |
| Drugmonizome | Kropiwnicki 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 |
| DrugQuest | Papanikolaou 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 |
| DrugRep | Gan J., Liu J., Liu Y., Chen S., Dai W., Xiao Z.-X., Cao Y., DrugRep: an automatic virtual screening server for drug repurposing. Acta Pharmacologica Sinica, 2022, doi: 10.1038/s41401-022-00996-2. 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 Profiler | Tanoli 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 Engine | Park 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 |
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Last Updated on 17-04-2024 by Piotr Minkiewicz