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ORCIDJournal of Cheminformatics, Volume 8
Volume 8, Number 1, December 2016
- Ludovic Chaput, Juan Martinez-Sanz, Eric Quiniou
, Pascal Rigolet, Nicolas Saettel, Liliane Mouawad:
vSDC: a method to improve early recognition in virtual screening when limited experimental resources are available. 1:1-1:18 - Igor V. Tetko, Daniel M. Lowe, Antony J. Williams:
The development of models to predict melting and pyrolysis point data associated with several hundred thousand compounds mined from PATENTS. 2:1-2:18 - Christoph Ruttkies, Emma Schymanski, Sebastian Wolf, Juliane Hollender, Steffen Neumann:
MetFrag relaunched: incorporating strategies beyond in silico fragmentation. 3:1-3:16 - Wilmer Leal, Eugenio-José Llanos, Guillermo Restrepo, Carlos F. Suárez, Manuel-Elkin Patarroyo:
How frequently do clusters occur in hierarchical clustering analysis? A graph theoretical approach to studying ties in proximity. 4:1-4:16 - Sebastian Böcker, Kai Dührkop:
Fragmentation trees reloaded. 5:1-5:26 - Tailong Lei, Youyong Li, Yunlong Song, Dan Li, Huiyong Sun, Tingjun Hou:
ADMET evaluation in drug discovery: 15. Accurate prediction of rat oral acute toxicity using relevance vector machine and consensus modeling. 6:1-6:19 - Floriane Montanari, Barbara Zdrazil, Daniela Digles, Gerhard F. Ecker:
Selectivity profiling of BCRP versus P-gp inhibition: from automated collection of polypharmacology data to multi-label learning. 7:1-7:13 - David M. L. Brown, Herman Cho, Wibe A. de Jong:
Bridging experiment and theory: a template for unifying NMR data and electronic structure calculations. 8:1-8:9 - Cerys Willoughby, Thomas A. Logothetis, Jeremy G. Frey:
Effects of using structured templates for recalling chemistry experiments. 9:1-9:17 - César R. García-Jacas, Ernesto Contreras-Torres, Yovani Marrero-Ponce, Mario Pupo-Meriño, Stephen J. Barigye, Lisset Cabrera-Leyva:
Examining the predictive accuracy of the novel 3D N-linear algebraic molecular codifications on benchmark datasets. 10:1-10:16 - Neil Swainston, Janna Hastings, Adriano Dekker, Venkatesh Muthukrishnan, John W. May, Christoph Steinbeck, Pedro Mendes:
libChEBI: an API for accessing the ChEBI database. 11:1-11:6 - P. B. Jayaraj, Mathias K. Ajay, M. Nufail, G. Gopakumar, U. C. Abdul Jaleel:
GPURFSCREEN: a GPU based virtual screening tool using random forest classifier. 12:1-12:10 - Isidro Cortes-Ciriano:
Bioalerts: a python library for the derivation of structural alerts from bioactivity and toxicity data sets. 13:1-13:6 - Misagh Naderi, Chris Alvin, Yun Ding, Supratik Mukhopadhyay, Michal Brylinski:
A graph-based approach to construct target-focused libraries for virtual screening. 14:1-14:16 - Wail Ba-alawi, Othman Soufan, Magbubah Essack, Panos Kalnis, Vladimir B. Bajic:
DASPfind: new efficient method to predict drug-target interactions. 15:1-15:9 - Gergely Zahoránszky-Köhalmi, Cristian Bologa, Oleg Ursu, Tudor I. Oprea:
Impact of similarity threshold on the topology of molecular similarity networks and clustering outcomes. 16:1-16:17 - Kirill Okhotnikov, Thibault Charpentier, Sylvian Cadars:
Supercell program: a combinatorial structure-generation approach for the local-level modeling of atomic substitutions and partial occupancies in crystals. 17:1-17:15 - 11th German Conference on Chemoinformatics (GCC 2015) - Fulda, Germany. 8-10 November 2015. 18:1-18:27
- Gabriel Núñez-Vivanco, Alejandro Valdés-Jiménez, Felipe Besoain, Miguel Reyes-Parada:
Geomfinder: a multi-feature identifier of similar three-dimensional protein patterns: a ligand-independent approach. 19:1-19:15 - Zhonghua Wang, Lu Liang, Zheng Yin, Jianping Lin:
Improving chemical similarity ensemble approach in target prediction. 20:1-20:10 - Joachim Baumeister, Albrecht Striffler, Marc Brandt, Michael Neumann:
Collaborative decision support and documentation in chemical safety with KnowSEC. 21:1-21:16 - Boris L. Alperin, Andrey O. Kuzmin, Ludmila Yu. Ilina, Vladimir D. Gusev, Natalia V. Salomatina, Valentin N. Parmon:
Terminology spectrum analysis of natural-language chemical documents: term-like phrases retrieval routine. 22:1-22:17 - Yu Du, Tieliu Shi:
Ligand cluster-based protein network and ePlatton, a multi-target ligand finder. 23:1-23:12 - Ting Gao, Hong-Zhi Li, Wenze Li, Lin Li, Chao Fang, Hui Li, Li Hong Hu, Yinghua Lu, Zhongmin Su:
A machine learning correction for DFT non-covalent interactions based on the S22, S66 and X40 benchmark databases. 24:1-24:17 - Mahendra Awale, Jean-Louis Reymond:
Web-based 3D-visualization of the DrugBank chemical space. 25:1-25:8 - Andrés M. Castillo, Andrés Bernal, Reiner Dieden, Luc Patiny, Julien Wist:
"Ask Ernö": a self-learning tool for assignment and prediction of nuclear magnetic resonance spectra. 26:1-26:8 - Mathew R. Koebel, Grant Schmadeke, Richard G. Posner, Suman Sirimulla:
AutoDock VinaXB: implementation of XBSF, new empirical halogen bond scoring function, into AutoDock Vina. 27:1-27:8 - Gergely Zahoránszky-Köhalmi, Cristian Bologa, Oleg Ursu, Tudor I. Oprea:
Erratum to: Impact of similarity threshold on the topology of molecular similarity networks and clustering outcomes. 28:1 - Jeremy J. Yang, Oleg Ursu, Christopher A. Lipinski, Larry A. Sklar, Tudor I. Oprea, Cristian Bologa:
Badapple: promiscuity patterns from noisy evidence. 29:1-29:14 - Jean-Paul Ebejer, Michael H. Charlton, Paul W. Finn:
Are the physicochemical properties of antibacterial compounds really different from other drugs? 30:1-30:9 - Jakub Galgonek, Tomás Hurt, Vendula Michlíková, Petr Onderka, Jan Schwarz, Jirí Vondrásek:
Advanced SPARQL querying in small molecule databases. 31:1-31:14 - Sunghwan Kim, Paul A. Thiessen, Tiejun Cheng, Bo Yu, Benjamin A. Shoemaker, Jiyao Wang, Evan Bolton, Yanli Wang, Stephen H. Bryant:
Literature information in PubChem: associations between PubChem records and scientific articles. 32:1-32:15 - Ashenafi Legehar, Henri Xhaard, Leo Ghemtio:
IDAAPM: integrated database of ADMET and adverse effects of predictive modeling based on FDA approved drug data. 33:1-33:11 - Jie Dong, Zhi-Jiang Yao, Ming Wen, Min-Feng Zhu, Ning-Ning Wang, Hongyu Miao, Aiping Lu, Wen-Bin Zeng, Dong-Sheng Cao:
BioTriangle: a web-accessible platform for generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions. 34:1-34:13 - Santiago Vilar, George Hripcsak:
Leveraging 3D chemical similarity, target and phenotypic data in the identification of drug-protein and drug-adverse effect associations. 35:1-35:12 - Noel M. O'Boyle, Roger A. Sayle:
Comparing structural fingerprints using a literature-based similarity benchmark. 36:1-36:14 - Ming Hao, Stephen H. Bryant, Yanli Wang:
Cheminformatics analysis of the AR agonist and antagonist datasets in PubChem. 37:1-37:13 - Jun Gao, Qingchen Zhang, Min Liu, Lixin Zhu, Dingfeng Wu, Zhiwei Cao, Ruixin Zhu:
bSiteFinder, an improved protein-binding sites prediction server based on structural alignment: more accurate and less time-consuming. 38:1-38:10 - Jonathan Alvarsson, Samuel Lampa, Wesley Schaal, Claes R. Andersson, Jarl E. S. Wikberg, Ola Spjuth:
Large-scale ligand-based predictive modelling using support vector machines. 39:1-39:9 - Maciej Barycki, Anita Sosnowska, Magdalena Piotrowska, Piotr Urbaszek, Anna Rybinska, Monika Grzonkowska, Tomasz Puzyn:
ILPC: simple chemometric tool supporting the design of ionic liquids. 40:1-40:14 - Varsha S. Kulkarni, David J. Wild:
An activity canyon characterization of the pharmacological topography. 41:1-41:12 - Gert-Jan Bekker, Haruki Nakamura, Akira R. Kinjo:
Molmil: a molecular viewer for the PDB and beyond. 42:1-42:5 - Nathalie Lagarde, Solenne Delahaye, Jean-François Zagury, Matthieu Montès:
Discriminating agonist and antagonist ligands of the nuclear receptors using 3D-pharmacophores. 43:1-43:18 - Amy McMillan, Justin B. Renaud, Gregory B. Gloor, Gregor Reid, Mark W. Sumarah:
Post-acquisition filtering of salt cluster artefacts for LC-MS based human metabolomic studies. 44:1-44:5 - Sakari Lätti, Sanna P. Niinivehmas, Olli T. Pentikäinen:
Rocker: Open source, easy-to-use tool for AUC and enrichment calculations and ROC visualization. 45:1-45:5 - Athira Dilip, Samo Lesnik, Tanja Stular, Dusanka Janezic, Janez Konc:
Ligand-based virtual screening interface between PyMOL and LiSiCA. 46:1-46:5 - Ola Spjuth, Patrik Rydberg, Egon L. Willighagen, Chris T. A. Evelo, Nina Jeliazkova:
XMetDB: an open access database for xenobiotic metabolism. 47:1-47:8 - Prachi Pradeep, Richard J. Povinelli, Shannon White, Stephen J. Merrill:
An ensemble model of QSAR tools for regulatory risk assessment. 48:1-48:9 - Andrea Mauri, Davide Ballabio, Roberto Todeschini, Viviana Consonni:
Mixtures, metabolites, ionic liquids: a new measure to evaluate similarity between complex chemical systems. 49:1-49:3 - Robert M. Hanson:
Jmol SMILES and Jmol SMARTS: specifications and applications. 50:1-50:20 - Priyanka Banerjee, Vishal B. Siramshetty, Malgorzata N. Drwal, Robert Preissner:
Computational methods for prediction of in vitro effects of new chemical structures. 51:1-51:11 - Robin Haunschild, Andreas Barth, Werner Marx:
Evolution of DFT studies in view of a scientometric perspective. 52:1-52:12 - Yifan Peng, Chih-Hsuan Wei, Zhiyong Lu:
Improving chemical disease relation extraction with rich features and weakly labeled data. 53:1-53:12 - Stuart J. Chalk:
SciData: a data model and ontology for semantic representation of scientific data. 54:1-54:24 - Stuart J. Chalk:
The Open Spectral Database: an open platform for sharing and searching spectral data. 55:1-55:14 - Ludovic Chaput, Juan Martinez-Sanz, Nicolas Saettel, Liliane Mouawad:
Benchmark of four popular virtual screening programs: construction of the active/decoy dataset remains a major determinant of measured performance. 56:1-56:17 - Tomás Racek, Jana Pazúriková, Radka Svobodová Vareková, Stanislav Geidl, Ales Krenek, Francesco L. Falginella, Vladimír Horský, Václav Hejret, Jaroslav Koca:
NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges. 57:1-57:14 - Junaid Arshad, Alexander Hoffmann, Sandra Gesing, Richard Grunzke, Jens Krüger, Tamás Kiss, Sonja Herres-Pawlis, Gábor Terstyánszky:
Multi-level meta-workflows: new concept for regularly occurring tasks in quantum chemistry. 58:1-58:17 - Maryam Habibi, David Luis Wiegandt, Florian Schmedding, Ulf Leser:
Recognizing chemicals in patents: a comparative analysis. 59:1-59:15 - Martin Gütlein, Stefan Kramer:
Filtered circular fingerprints improve either prediction or runtime performance while retaining interpretability. 60:1-60:16 - Yannick Djoumbou, Roman Eisner, Craig Knox, Leonid L. Chepelev, Janna Hastings, Gareth I. Owen, Eoin Fahy, Christoph Steinbeck, Shankar Subramanian, Evan Bolton, Russell Greiner, David S. Wishart:
ClassyFire: automated chemical classification with a comprehensive, computable taxonomy. 61:1-61:20 - Sunghwan Kim, Evan Bolton, Stephen H. Bryant:
Similar compounds versus similar conformers: complementarity between PubChem 2-D and 3-D neighboring sets. 62:1-62:17 - Mariana González-Medina, Fernando D. Prieto-Martínez, John R. Owen, José L. Medina-Franco:
Consensus Diversity Plots: a global diversity analysis of chemical libraries. 63:1-63:11 - Othman Soufan, Wail Ba-alawi, Moataz Afeef, Magbubah Essack, Panos Kalnis, Vladimir B. Bajic:
DRABAL: novel method to mine large high-throughput screening assays using Bayesian active learning. 64:1-64:14 - Hugo López-Fernández, Gustavo de S. Pessôa, Marco A. Z. Arruda, José Luis Capelo-Martínez, Florentino Fdez-Riverola, Daniel Glez-Peña, Miguel Reboiro-Jato:
LA-iMageS: a software for elemental distribution bioimaging using LA-ICP-MS data. 65:1-65:10 - Vincent F. Scalfani, Antony J. Williams, Valery Tkachenko, Karen Karapetyan, Alexey Pshenichnov, Robert M. Hanson, Jahred M. Liddie, Jason E. Bara:
Programmatic conversion of crystal structures into 3D printable files using Jmol. 66:1-66:8 - Samuel Lampa, Jonathan Alvarsson, Ola Spjuth:
Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles. 67:1-67:12 - Anastasia V. Rudik, Alexander V. Dmitriev, Alexey Lagunin, Dmitry Filimonov, Vladimir Poroikov:
Prediction of reacting atoms for the major biotransformation reactions of organic xenobiotics. 68:1-68:9 - Natália Aniceto, Alex Alves Freitas, Andreas Bender, Taravat Ghafourian:
A novel applicability domain technique for mapping predictive reliability across the chemical space of a QSAR: reliability-density neighbourhood. 69:1-69:20 - Joshua Meyers, Nathan Brown, Julian Blagg:
Mapping the 3D structures of small molecule binding sites. 70:1-70:13 - Yunuscan Kocak, Tansel Özyer, Reda Alhajj:
Utilizing maximal frequent itemsets and social network analysis for HIV data analysis. 71:1-71:15 - Saw Simeon, Watshara Shoombuatong, Nuttapat Anuwongcharoen, Likit Preeyanon, Virapong Prachayasittikul, Jarl E. S. Wikberg, Chanin Nantasenamat:
osFP: a web server for predicting the oligomeric states of fluorescent proteins. 72:1-72:15 - Muthukumarasamy Karthikeyan, Renu Vyas:
ChemEngine: harvesting 3D chemical structures of supplementary data from PDF files. 73:1-73:13 - Jakub Velkoborsky, David Hoksza:
Scaffold analysis of PubChem database as background for hierarchical scaffold-based visualization. 74:1-74:14
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