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Journal of Cheminformatics, Volume 7
Volume 7, 2015
- Isidro Cortes-Ciriano
, Daniel S. Murrell, Gerard J. P. van Westen
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
When drug discovery meets web search: Learning to Rank for ligand-based virtual screening. 5 - Alex Alves Freitas
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
eTOXlab, an open source modeling framework for implementing predictive models in production environments. 8 - Alex M. Clark
Machines first, humans second: on the importance of algorithmic interpretation of open chemistry data. 9 - Peter Ertl
Wikipedia Chemical Structure Explorer: substructure and similarity searching of molecules from Wikipedia. 10 - Alberto Gobbi
Atom-Atom-Path similarity and Sphere Exclusion clustering: tools for prioritizing fragment hits. 11 - Radoslav Krivák
Improving protein-ligand binding site prediction accuracy by classification of inner pocket points using local features. 12 - Stefan Mordalski
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
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
Why is Tanimoto index an appropriate choice for fingerprint-based similarity calculations? 20:1-20:13 - Tamer M. Ibrahim
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
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
Open Drug Discovery Toolkit (ODDT): a new open-source player in the drug discovery field. 26:1-26:6 - Hamse Y. Mussa, David Marcus
Verifying the fully "Laplacianised" posterior Naïve Bayesian approach and more. 27:1-27:11 - Parisa Amani
A practical Java tool for small-molecule compound appraisal. 28:1-28:4 - Rowan Hatherley, David K. Brown, Thommas M. Musyoka
SANCDB: a South African natural compound database. 29:1-29:9 - Karen Karapetyan
The Chemical Validation and Standardization Platform (CVSP): large-scale automated validation of chemical structure datasets. 30:1-30:13 - Lora Mak
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
PubChem structure-activity relationship (SAR) clusters. 33:1-33:22 - Gang Fu, Colin R. Batchelor
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
Synergy Maps: exploring compound combinations using network-based visualization. 36:1-36:11 - Matthew J. Harvey
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
Robust optimization of SVM hyperparameters in the classification of bioactive compounds. 38:1-38:15 - María Jimena Martínez
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
PubChem atom environments. 41:1-41:37 - Mohammad ElGamacy
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
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
MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics. 44:1-44:8 - Daniel S. Murrell, Isidro Cortes-Ciriano
Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules. 45:1-45:10 - Georgia Tsiliki
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
Managing expectations: assessment of chemistry databases generated by automated extraction of chemical structures from patents. 49:1-49:12 - Crina-Maria Ionescu, David Sehnal
AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules. 50:1-50:13 - Lewis H. Mervin
Target prediction utilising negative bioactivity data covering large chemical space. 51:1-51:16 - Charly Empereur-mot
Predictiveness curves in virtual screening. 52:1-52:17 - Yan Ma, Tobias Kind
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
Ambiguity of non-systematic chemical identifiers within and between small-molecule databases. 54:1-54:10 - Xiang Yu, Lewis Y. Geer
Target enhanced 2D similarity search by using explicit biological activity annotations and profiles. 55:1-55:12 - Mohamad Mohebifar
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
A note on utilising binary features as ligand descriptors. 58:1-58:3 - Stanislav Geidl, Tomás Bouchal
High-quality and universal empirical atomic charges for chemoinformatics applications. 59:1-59:10 - Jie Dong
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
Smiles2Monomers: a link between chemical and biological structures for polymers. 62:1-62:11 - Alessandro Lusci, Michael R. Browning, David Fooshee, S. Joshua Swamidass
Accurate and efficient target prediction using a potency-sensitive influence-relevance voter. 63:1-63:13
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