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ORCIDJournal of Cheminformatics, Volume 7
Volume 7, 2015
- Isidro Cortes-Ciriano
, Daniel S. Murrell, Gerard J. P. van Westen, Andreas Bender, Thérèse E. Malliavin:
Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling. 1 - Alexander Dörr, Lars Rosenbaum, Andreas Zell:
A ranking method for the concurrent learning of compounds with various activity profiles. 2 - Mahendra Awale, Xian Jin, Jean-Louis Reymond:
Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints. 3 - Ruifeng Liu, Xueping Yu, Anders Wallqvist:
Data-driven identification of structural alerts for mitigating the risk of drug-induced human liver injuries. 4 - Wei Zhang, Lijuan Ji, Yanan Chen, Kailin Tang, Haiping Wang, Ruixin Zhu, Wei Jia, Zhiwei Cao, Qi Liu:
When drug discovery meets web search: Learning to Rank for ligand-based virtual screening. 5 - Alex Alves Freitas, Kriti Limbu, Taravat Ghafourian:
Predicting volume of distribution with decision tree-based regression methods using predicted tissue: plasma partition coefficients. 6 - Karen A. Ryall, Aik Choon Tan:
Systems biology approaches for advancing the discovery of effective drug combinations. 7 - Pau Carrió, Oriol López, Ferran Sanz, Manuel Pastor:
eTOXlab, an open source modeling framework for implementing predictive models in production environments. 8 - Alex M. Clark, Antony J. Williams, Sean Ekins:
Machines first, humans second: on the importance of algorithmic interpretation of open chemistry data. 9 - Peter Ertl, Luc Patiny, Thomas Sander, Christian Rufener, Michaël Zasso:
Wikipedia Chemical Structure Explorer: substructure and similarity searching of molecules from Wikipedia. 10 - Alberto Gobbi, Anthony M. Giannetti, Huifen Chen, Man-Ling Lee:
Atom-Atom-Path similarity and Sphere Exclusion clustering: tools for prioritizing fragment hits. 11 - Radoslav Krivák, David Hoksza:
Improving protein-ligand binding site prediction accuracy by classification of inner pocket points using local features. 12 - Stefan Mordalski, Jagna Witek, Sabina Smusz, Krzysztof Rataj, Andrzej J. Bojarski:
Multiple conformational states in retrospective virtual screening - homology models vs. crystal structures: beta-2 adrenergic receptor case study. 13 - Chao Chen, Yang He, Jianhui Wu, Jinming Zhou:
Creation of a free, Internet-accessible database: the Multiple Target Ligand Database. 14:1-14:8 - Shardul Paricharak, Isidro Cortes-Ciriano, Adriaan P. IJzerman, Therese E. Malliavin, Andreas Bender:
Proteochemometric modelling coupled to in silico target prediction: an integrated approach for the simultaneous prediction of polypharmacology and binding affinity/potency of small molecules. 15 - Goran Kovacevic, Valera Veryazov:
Luscus: molecular viewer and editor for MOLCAS. 16:1-16:10 - Stephan Beisken, Pablo Conesa, Kenneth Haug, Reza M. Salek, Christoph Steinbeck:
SpeckTackle: JavaScript charts for spectroscopy. 17:1-17:6 - Wei Pan Feinstein, Michal Brylinski:
Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets. 18:1-18:10 - Jiangyong Gu, Xinzhuang Zhang, Yimin Ma, Na Li, Fang Luo, Liang Cao, Zhenzhong Wang, Gu Yuan, Lirong Chen, Wei Xiao, Xiaojie Xu:
Quantitative modeling of dose-response and drug combination based on pathway network. 19:1-19:10 - Dávid Bajusz, Anita Rácz, Károly Héberger:
Why is Tanimoto index an appropriate choice for fingerprint-based similarity calculations? 20:1-20:13 - Tamer M. Ibrahim, Matthias R. Bauer, Frank M. Boeckler:
Applying DEKOIS 2.0 in structure-based virtual screening to probe the impact of preparation procedures and score normalization. 21:1-21:16 - Michael A. Bauer, Daniel Berleant, Andrew P. Cornell, Robert E. Belford:
WikiHyperGlossary (WHG): an information literacy technology for chemistry documents. 22:1-22:16 - Stephen R. Heller, Alan McNaught, Igor V. Pletnev, Stephen Stein, Dmitrii Tchekhovskoi:
InChI, the IUPAC International Chemical Identifier. 23:1-23:34 - Avid M. Afzal, Hamse Y. Mussa, Richard E. Turner, Andreas Bender, Robert C. Glen:
A multi-label approach to target prediction taking ligand promiscuity into account. 24:1-24:14 - Chun-Wei Tung:
ChemDIS: a chemical-disease inference system based on chemical-protein interactions. 25:1-25:7 - Maciej Wójcikowski, Piotr Zielenkiewicz, Pawel Siedlecki:
Open Drug Discovery Toolkit (ODDT): a new open-source player in the drug discovery field. 26:1-26:6 - Hamse Y. Mussa, David Marcus, John B. O. Mitchell, Robert C. Glen:
Verifying the fully "Laplacianised" posterior Naïve Bayesian approach and more. 27:1-27:11 - Parisa Amani, Todd Sneyd, Sarah Preston, Neil D. Young, Lyndel Mason, Ulla-Maja Bailey, Jonathan B. Baell, David Camp, Robin B. Gasser, Alain-Dominique Gorse, Paul Taylor, Andreas Hofmann:
A practical Java tool for small-molecule compound appraisal. 28:1-28:4 - Rowan Hatherley, David K. Brown, Thommas M. Musyoka, David L. Penkler, Ngonidzashe Faya, Kevin A. Lobb, Özlem Tastan Bishop:
SANCDB: a South African natural compound database. 29:1-29:9 - Karen Karapetyan, Colin R. Batchelor, David Sharpe, Valery Tkachenko, Antony J. Williams:
The Chemical Validation and Standardization Platform (CVSP): large-scale automated validation of chemical structure datasets. 30:1-30:13 - Lora Mak, David Marcus, Andrew Howlett, Galina Yarova, Guus Duchateau, Werner Klaffke, Andreas Bender, Robert C. Glen:
Metrabase: a cheminformatics and bioinformatics database for small molecule transporter data analysis and (Q)SAR modeling. 31:1-31:12 - Villu Ruusmann, Sulev Sild, Uko Maran:
QSAR DataBank repository: open and linked qualitative and quantitative structure-activity relationship models. 32:1-32:11 - Sunghwan Kim, Lianyi Han, Bo Yu, Volker Hähnke, Evan Bolton, Stephen H. Bryant:
PubChem structure-activity relationship (SAR) clusters. 33:1-33:22 - Gang Fu, Colin R. Batchelor, Michel Dumontier, Janna Hastings, Egon L. Willighagen, Evan Bolton:
PubChemRDF: towards the semantic annotation of PubChem compound and substance databases. 34:1-34:15 - Melanie C. Burger:
ChemDoodle Web Components: HTML5 toolkit for chemical graphics, interfaces, and informatics. 35:1-35:7 - Richard Lewis, Rajarshi Guha, Tamás Korcsmáros, Andreas Bender:
Synergy Maps: exploring compound combinations using network-based visualization. 36:1-36:11 - Matthew J. Harvey, Nicholas J. Mason, Andrew McLean, Henry S. Rzepa:
Standards-based metadata procedures for retrieving data for display or mining utilizing persistent (data-DOI) identifiers. 37:1-37:10 - Wojciech M. Czarnecki, Sabina Podlewska, Andrzej J. Bojarski:
Robust optimization of SVM hyperparameters in the classification of bioactive compounds. 38:1-38:15 - María Jimena Martínez, Ignacio Ponzoni, Mónica Fátima Díaz, Gustavo E. Vazquez, Axel J. Soto:
Visual analytics in cheminformatics: user-supervised descriptor selection for QSAR methods. 39:1-39:17 - Abhik Seal, Yong-Yeol Ahn, David J. Wild:
Optimizing drug-target interaction prediction based on random walk on heterogeneous networks. 40:1-40:12 - Volker Hähnke, Evan Bolton, Stephen H. Bryant:
PubChem atom environments. 41:1-41:37 - Mohammad ElGamacy, Luc van Meervelt:
A fast topological analysis algorithm for large-scale similarity evaluations of ligands and binding pockets. 42:1-42:14 - Matthew J. Harvey, Nicholas J. Mason, Andrew McLean, Peter Murray-Rust, Henry S. Rzepa, James J. P. Stewart:
Standards-based curation of a decade-old digital repository dataset of molecular information. 43:1-43:14 - James G. Jeffryes, Ricardo L. Colastani, Mona Elbadawi-Sidhu, Tobias Kind, Thomas D. Niehaus, Linda J. Broadbelt, Andrew D. Hanson, Oliver Fiehn, Keith E. J. Tyo, Christopher S. Henry:
MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics. 44:1-44:8 - Daniel S. Murrell, Isidro Cortes-Ciriano, Gerard J. P. van Westen, Ian Stott, Andreas Bender, Thérèse E. Malliavin, Robert C. Glen:
Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules. 45:1-45:10 - Georgia Tsiliki, Cristian R. Munteanu, José A. Seoane, Carlos Fernandez-Lozano, Haralambos Sarimveis, Egon L. Willighagen:
RRegrs: an R package for computer-aided model selection with multiple regression models. 46:1-46:16 - Sandeepkumar Kothiwale, Jeffrey L. Mendenhall, Jens Meiler:
BCL: : Conf: small molecule conformational sampling using a knowledge based rotamer library. 47:1-47:15 - Janez Konc, Samo Lesnik, Dusanka Janezic:
Modeling enzyme-ligand binding in drug discovery. 48:1-48:8 - Stefan Senger, Luca Bartek, George Papadatos, Anna Gaulton:
Managing expectations: assessment of chemistry databases generated by automated extraction of chemical structures from patents. 49:1-49:12 - Crina-Maria Ionescu, David Sehnal, Francesco L. Falginella, Purbaj Pant, Lukás Pravda, Tomás Bouchal, Radka Svobodová Vareková, Stanislav Geidl, Jaroslav Koca:
AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules. 50:1-50:13 - Lewis H. Mervin, Avid M. Afzal, Georgios Drakakis, Richard Lewis, Ola Engkvist, Andreas Bender:
Target prediction utilising negative bioactivity data covering large chemical space. 51:1-51:16 - Charly Empereur-mot, Hélène Guillemain, Aurélien Latouche, Jean-François Zagury, Vivian Viallon, Matthieu Montès:
Predictiveness curves in virtual screening. 52:1-52:17 - Yan Ma, Tobias Kind, Arpana Vaniya, Ingrid Gennity, Johannes F. Fahrmann, Oliver Fiehn:
An in silico MS/MS library for automatic annotation of novel FAHFA lipids. 53:1-53:5 - Saber A. Akhondi, Sorel Muresan, Antony J. Williams, Jan A. Kors:
Ambiguity of non-systematic chemical identifiers within and between small-molecule databases. 54:1-54:10 - Xiang Yu, Lewis Y. Geer, Lianyi Han, Stephen H. Bryant:
Target enhanced 2D similarity search by using explicit biological activity annotations and profiles. 55:1-55:12 - Mohamad Mohebifar, Fatemehsadat Sajadi:
Chemozart: a web-based 3D molecular structure editor and visualizer platform. 56:1-56:8 - Kee-Choo Chung, Hwangseo Park:
Accuracy enhancement in the estimation of molecular hydration free energies by implementing the intramolecular hydrogen bond effects. 57:1-57:12 - Hamse Y. Mussa, John B. O. Mitchell, Robert C. Glen:
A note on utilising binary features as ligand descriptors. 58:1-58:3 - Stanislav Geidl, Tomás Bouchal, Tomás Racek, Radka Svobodová Vareková, Václav Hejret, Ales Krenek, Ruben Abagyan, Jaroslav Koca:
High-quality and universal empirical atomic charges for chemoinformatics applications. 59:1-59:10 - Jie Dong, Dong-Sheng Cao, Hongyu Miao, Shao Liu, Bai-Chuan Deng, Yong-Huan Yun, Ning-Ning Wang, Aiping Lu, Wen-Bin Zeng, Alex F. Chen:
ChemDes: an integrated web-based platform for molecular descriptor and fingerprint computation. 60:1-60:10 - Yocheved Gilad, Katalin Nadassy, Hanoch Senderowitz:
A reliable computational workflow for the selection of optimal screening libraries. 61:1-61:17 - Yoann Dufresne, Laurent Noé, Valérie Leclère, Maude Pupin:
Smiles2Monomers: a link between chemical and biological structures for polymers. 62:1-62:11 - Alessandro Lusci, Michael R. Browning, David Fooshee, S. Joshua Swamidass, Pierre Baldi:
Accurate and efficient target prediction using a potency-sensitive influence-relevance voter. 63:1-63:13
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