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ORCIDJournal of Cheminformatics, Volume 6
Volume 6, Number 1, 2014
- Ala Qabaja, Mohammed Alshalalfa, Eisa Alanazi
, Reda Alhajj:
Prediction of novel drug indications using network driven biological data prioritization and integration. 1 - Hulda S. Haraldsdóttir, Ines Thiele, Ronan M. T. Fleming:
Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2. 2 - John W. May, Christoph Steinbeck:
Efficient ring perception for the Chemistry Development Kit. 3 - Julien C. Thibault, Daniel R. Roe, Julio C. Facelli, Thomas E. Cheatham III:
Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing. 4 - Pedro Franco, Nuria Porta, John D. Holliday, Peter Willett:
The use of 2D fingerprint methods to support the assessment of structural similarity in orphan drug legislation. 5 - Sven Kochmann:
Beryllium10: a free and simple tool for creating and managing group safety data sheets. 6 - David Hoksza, Petr Skoda, Milan Vorsilák, Daniel Svozil:
Molpher: a software framework for systematic chemical space exploration. 7 - Samuel J. Webb, Thierry Hanser, Brendan J. Howlin, Paul Krause, Jonathan D. Vessey:
Feature combination networks for the interpretation of statistical machine learning models: application to Ames mutagenicity. 8 - Andrés M. Castillo, Andrés Bernal, Luc Patiny, Julien Wist:
A new method for the comparison of 1H NMR predictors based on tree-similarity of spectra. 9 - Damjan Krstajic, Ljubomir J. Buturovic, David E. Leahy, Simon Thomas:
Cross-validation pitfalls when selecting and assessing regression and classification models. 10 - Rajarshi Guha, José L. Medina-Franco:
On the validity versus utility of activity landscapes: are all activity cliffs statistically significant? 11 - Stefan Bietz, Sascha Urbaczek, Benjamin Schulz, Matthias Rarey:
Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes. 12 - Jinlong Ru, Peng Li, Jinan Wang, Wei Zhou, Bohui Li, Chao Huang, Pidong Li, Zihu Guo, Weiyang Tao, Yinfeng Yang, Xue Xu, Yan Li, Yonghua Wang, Ling Yang:
TCMSP: a database of systems pharmacology for drug discovery from herbal medicines. 13 - Bingjie Hu, Markus A. Lill:
PharmDock: a pharmacophore-based docking program. 14 - Jakub Galgonek, Jirí Vondrásek:
On InChI and evaluating the quality of cross-reference links. 15 - Bharath Srinivasan, Hongyi Zhou, Julia Kubanek, Jeffrey Skolnick:
Experimental validation of FINDSITEcomb virtual ligand screening results for eight proteins yields novel nanomolar and micromolar binders. 16 - Safaa Eltyeb, Naomie Salim:
Chemical named entities recognition: a review on approaches and applications. 17 - Mark I. Borkum, Jeremy G. Frey:
Usage and applications of Semantic Web techniques and technologies to support chemistry research. 18 - Ali Ahmed, Faisal Saeed, Naomie Salim, Ammar Abdo:
Condorcet and borda count fusion method for ligand-based virtual screening. 19 - Svetlana I. Ovchinnikova, Arseniy A. Bykov, Aslan Yu. Tsivadze, Evgeny P. Dyachkov, Natalia V. Kireeva:
Supervised extensions of chemography approaches: case studies of chemical liabilities assessment. 20 - Thierry Hanser, Chris Barber, Edward Rosser, Jonathan D. Vessey, Samuel J. Webb, Stéphane Werner:
Self organising hypothesis networks: a new approach for representing and structuring SAR knowledge. 21 - Matthew D. Krasowski, Sean Ekins:
Using cheminformatics to predict cross reactivity of "designer drugs" to their currently available immunoassays. 22 - Francois Berenger, Arnout R. D. Voet, Xiao Yin Lee, Kam Y. J. Zhang:
A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening. 23 - Antonino Fiannaca, Massimo La Rosa, Giuseppe Di Fatta, Salvatore Gaglio, Riccardo Rizzo, Alfonso Urso:
The BioDICE Taverna plugin for clustering and visualization of biological data: a workflow for molecular compounds exploration. 24 - Villu Ruusmann, Sulev Sild, Uko Maran:
QSAR DataBank - an approach for the digital organization and archiving of QSAR model information. 25 - Jing Lu, Jianlong Peng, Jinan Wang, Qiancheng Shen, Yi Bi, Likun Gong, Mingyue Zheng, Xiaomin Luo, Weiliang Zhu, Hualiang Jiang, Kaixian Chen:
Estimation of acute oral toxicity in rat using local lazy learning. 26 - Lars Ruddigkeit, Mahendra Awale, Jean-Louis Reymond:
Expanding the fragrance chemical space for virtual screening. 27 - Xia Wang, Haipeng Chen, Feng Yang, Jiayu Gong, Shiliang Li, Jianfeng Pei, Xiaofeng Liu, Hualiang Jiang, Luhua Lai, Honglin Li:
iDrug: a web-accessible and interactive drug discovery and design platform. 28 - Jonathan D. Tyzack, Hamse Y. Mussa, Mark J. Williamson, Johannes Kirchmair, Robert C. Glen:
Cytochrome P450 site of metabolism prediction from 2D topological fingerprints using GPU accelerated probabilistic classifiers. 29 - Martin Bogdan, Dominik Brugger, Wolfgang Rosenstiel, Bernd Speiser:
Estimation of diffusion coefficients from voltammetric signals by support vector and gaussian process regression. 30 - Masaki Suzuki, Hiroshi Nagamochi, Tatsuya Akutsu:
Efficient enumeration of monocyclic chemical graphs with given path frequencies. 31 - Rafal Kurczab, Sabina Smusz, Andrzej J. Bojarski:
The influence of negative training set size on machine learning-based virtual screening. 32 - Xian Liu, Yuan Xu, Shanshan Li, Yulan Wang, Jianlong Peng, Cheng Luo, Xiaomin Luo, Mingyue Zheng, Kaixian Chen, Hualiang Jiang:
In Silico target fishing: addressing a "Big Data" problem by ligand-based similarity rankings with data fusion. 33 - Robert D. Clark, Wenkel Liang, Adam C. Lee, Michael S. Lawless, Robert Fraczkiewicz, Marvin Waldman:
Using beta binomials to estimate classification uncertainty for ensemble models. 34 - Isidro Cortes-Ciriano, Gerard J. P. van Westen, Eelke B. Lenselink, Daniel S. Murrell, Andreas Bender, Thérèse E. Malliavin:
Proteochemometric modeling in a Bayesian framework. 35 - Qian Zhang, Wei Zhang, Youyong Li, Junmei Wang, Jian Zhang, Tingjun Hou:
MORT: a powerful foundational library for computational biology and CADD. 36 - Paolo Tosco, Nikolaus Stiefl, Gregory A. Landrum:
Bringing the MMFF force field to the RDKit: implementation and validation. 37 - Alex M. Clark, Malabika Sarker, Sean Ekins:
New target prediction and visualization tools incorporating open source molecular fingerprints for TB Mobile 2.0. 38 - Matteo Floris, Alberto Manganaro, Orazio Nicolotti, Ricardo Medda, Giuseppe Felice Mangiatordi, Emilio Benfenati:
A generalizable definition of chemical similarity for read-across. 39 - George Papadatos, Gerard J. P. van Westen, Samuel Croset, Rita Santos, Simone Trubian, John P. Overington:
A document classifier for medicinal chemistry publications trained on the ChEMBL corpus. 40 - Martin Gütlein, Andreas Karwath, Stefan Kramer:
CheS-Mapper 2.0 for visual validation of (Q)SAR models. 41 - Sorin I. Avram, Simona Funar-Timofei, Ana Borota, Sridhar Chennamaneni, Anil Manchala, Sorel Muresan:
Quantitative estimation of pesticide-likeness for agrochemical discovery. 42 - Jon Chambers, Mark Davies, Anna Gaulton, George Papadatos, Anne Hersey, John P. Overington:
UniChem: extension of InChI-based compound mapping to salt, connectivity and stereochemistry layers. 43 - Ctibor Skuta, Petr Bartunek, Daniel Svozil:
InCHlib - interactive cluster heatmap for web applications. 44 - Andreas Truszkowski, Mirco Daniel, Hubert Kuhn, Stefan Neumann, Christoph Steinbeck, Achim Zielesny, Matthias Epple:
A molecular fragment cheminformatics roadmap for mesoscopic simulation. 45 - Arun Sharma, Prasun Dutta, Maneesh Sharma, Neeraj Rajput, Bhavna Dodiya, John J. Georrge, Trupti Kholia, Anshu Bhardwaj:
BioPhytMol: a drug discovery community resource on anti-mycobacterial phytomolecules and plant extracts. 46 - Désirée Baumann, Knut Baumann:
Reliable estimation of prediction errors for QSAR models under model uncertainty using double cross-validation. 47 - Yurii Sushko, Sergii Novotarskyi, Robert Körner, Joachim Vogt, Ahmed Abdelaziz, Igor V. Tetko:
Prediction-driven matched molecular pairs to interpret QSARs and aid the molecular optimization process. 48
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