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Journal of Cheminformatics, Volume 5
Volume 5, 2013
- Sunghwan Kim
, Evan Bolton
PubChem3D: conformer ensemble accuracy. 1 - Abhik Seal, Perumal Yogeeswari, Dharmaranjan Sriram, David J. Wild:
Enhanced ranking of PknB Inhibitors using data fusion methods. 2 - Jon Chambers, Mark Davies
UniChem: a unified chemical structure cross-referencing and identifier tracking system. 3 - Ioana Oprisiu, Sergii Novotarskyi, Igor V. Tetko
Modeling of non-additive mixture properties using the Online CHEmical database and Modeling environment (OCHEM). 4 - Sheng Tian
Drug-likeness analysis of traditional Chinese medicines: 2. Characterization of scaffold architectures for drug-like compounds, non-drug-like compounds, and natural compounds from traditional Chinese medicines. 5 - Henry S. Rzepa
Chemical datuments as scientific enablers. 6 - Stephen R. Heller, Alan McNaught, Stephen Stein, Dmitrii Tchekhovskoi, Igor V. Pletnev
InChI - the worldwide chemical structure identifier standard. 7 - Hwanho Choi, Hongsuk Kang, Hwangseo Park:
New solvation free energy function comprising intermolecular solvation and intramolecular self-solvation terms. 8 - Ana L. Teixeira, João Paulo Leal
Random forests for feature selection in QSPR Models - an application for predicting standard enthalpy of formation of hydrocarbons. 9 - Christopher Southan
InChI in the wild: An Assessment of InChIKey searching in Google. 10 - Sunil Sagar, Mandeep Kaur
Dragon exploration system on marine sponge compounds interactions. 11 - Kerstin Scheubert, Franziska Hufsky
Computational mass spectrometry for small molecules. 12 - Sean Ekins, Alex M. Clark
TB mobile: a mobile app for anti-tuberculosis molecules with known targets. 13 - Ola Spjuth
Applications of the InChI in cheminformatics with the CDK and Bioclipse. 14 - Naoto Takada, Norihito Ohmori, Takashi Okada:
Mining basic active structures from a large-scale database. 15 - Anna Palczewska, Daniel Neagu
Using Pareto points for model identification in predictive toxicology. 16 - Sabina Smusz
The influence of the inactives subset generation on the performance of machine learning methods. 17 - Radka Svobodová Vareková
Predicting pKa values from EEM atomic charges. 18 - Melvin J. Yu:
Druggable chemical space and enumerative combinatorics. 19 - Christopher Southan
Extracting and connecting chemical structures from text sources using chemicalize.org. 20 - Ying-Ting Lin:
A tandem regression-outlier analysis of a ligand cellular system for key structural modifications around ligand binding. 21 - Effirul Ikhwan Ramlan
In-silico design of computational nucleic acids for molecular information processing. 22 - Egon L. Willighagen
The ChEMBL database as linked open data. 23 - Bruno Bienfait, Peter Ertl
JSME: a free molecule editor in JavaScript. 24:1-24:6 - Wibe A. de Jong
From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language. 25 - Sereina Riniker
Open-source platform to benchmark fingerprints for ligand-based virtual screening. 26 - Faizan Sahigara, Davide Ballabio
Defining a novel k-nearest neighbours approach to assess the applicability domain of a QSAR model for reliable predictions. 27 - Hong Kang, Kailin Tang
HIM-herbal ingredients in-vivo metabolism database. 28 - Christoph Steinbeck:
Review of "Contemporary computer-assisted approaches to molecular structure elucidation (new developments in NMR)" by Mikhail E Elyashberg, Antony Williams and Kirill Blinov. 29 - Francesco Napolitano
Drug Repositioning: A Machine-Learning Approach through Data Integration. 30 - Lazaros Mavridis
Predicting the protein targets for athletic performance-enhancing substances. 31 - David J. Wild:
Cheminformatics for the masses: a chance to increase educational opportunities for the next generation of cheminformaticians. 32 - Lars Rosenbaum, Alexander Dörr, Matthias R. Bauer
Inferring multi-target QSAR models with taxonomy-based multi-task learning. 33 - Xiaohui Qu, Diogo A. R. S. Latino, João Aires-de-Sousa
A big data approach to the ultra-fast prediction of DFT-calculated bond energies. 34 - Robert Smith, Ryan Williamson, Dan Ventura, John T. Prince
Rubabel: Wrapping OpenBabel with Ruby. 35 - Adrià Cereto-Massagué
The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites. 36 - Hamse Y. Mussa, John B. O. Mitchell, Robert C. Glen:
Full "Laplacianised" posterior naive Bayesian algorithm. 37 - Matthias Hilbig, Sascha Urbaczek, Inken Groth, Stefan Heuser, Matthias Rarey:
MONA - Interactive manipulation of molecule collections. 38 - David Sehnal, Radka Svobodová Vareková, Karel Berka, Lukás Pravda, Veronika Navrátilová, Pavel Banás, Crina-Maria Ionescu, Michal Otyepka, Jaroslav Koca:
MOLE 2.0: advanced approach for analysis of biomacromolecular channels. 39 - Ségolène Caboche:
LeView: automatic and interactive generation of 2D diagrams for biomacromolecule/ligand interactions. 40 - Gerard J. P. van Westen, Remco F. Swier, Jörg K. Wegner
Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets. 41 - Gerard J. P. van Westen
Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets. 42 - Sereina Riniker
Similarity maps - a visualization strategy for molecular fingerprints and machine-learning methods. 43 - Gus R. Rosania, Kerby Shedden, Nan Zheng, Xinyuan Zhang
Visualizing chemical structure-subcellular localization relationships using fluorescent small molecules as probes of cellular transport. 44 - Guenter Grethe, Jonathan M. Goodman
International chemical identifier for reactions (RInChI). 45 - Clarke W. Earley:
CH5M3D: an HTML5 program for creating 3D molecular structures. 46 - Svetoslav H. Slavov, Bruce A. Pearce, Dan A. Buzatu, Jon G. Wilkes, Richard D. Beger:
Complementary PLS and KNN algorithms for improved 3D-QSDAR consensus modeling of AhR binding. 47 - Joos Kiener:
Molecule database framework: a framework for creating database applications with chemical structure search capability. 48 - Shardul Paricharak, Tom Klenka, Martin Augustin, Umesh A. Patel, Andreas Bender:
Are phylogenetic trees suitable for chemogenomics analyses of bioactivity data sets: the importance of shared active compounds and choosing a suitable data embedding method, as exemplified on Kinases. 49 - Tobias Girschick, Lucia Puchbauer, Stefan Kramer:
Improving structural similarity based virtual screening using background knowledge. 50 - Jiangyong Gu, Yuanshen Gui, Lirong Chen, Gu Yuan, Xiaojie Xu:
CVDHD: a cardiovascular disease herbal database for drug discovery and network pharmacology. 51 - Simon J. Coles
First steps towards semantic descriptions of electronic laboratory notebook records. 52
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