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  1. The rampant increase of public bioactivity databases has fostered the development of computational chemogenomics methodologies to evaluate potential ligand-target interactions (polypharmacology) both in a qual...

    Authors: Shardul Paricharak, Isidro Cortés-Ciriano, Adriaan P IJzerman, Thérèse E Malliavin and Andreas Bender
    Citation: Journal of Cheminformatics 2015 7:15
    Content type: Research article Published on:

  2. Distinguishing active from inactive compounds is one of the crucial problems of molecular docking, especially in the context of virtual screening experiments. The randomization of poses and the natural flexibi...

    Authors: Stefan Mordalski, Jagna Witek, Sabina Smusz, Krzysztof Rataj and Andrzej J Bojarski
    Citation: Journal of Cheminformatics 2015 7:13
    Content type: Research article Published on:

  3. Protein-ligand binding site prediction from a 3D protein structure plays a pivotal role in rational drug design and can be helpful in drug side-effects prediction or elucidation of protein function. Embedded w...

    Authors: Radoslav Krivák and David Hoksza
    Citation: Journal of Cheminformatics 2015 7:12
    Content type: Research Article Published on:

  4. After performing a fragment based screen the resulting hits need to be prioritized for follow-up structure elucidation and chemistry. This paper describes a new similarity metric, Atom-Atom-Path (AAP) similari...

    Authors: Alberto Gobbi, Anthony M Giannetti, Huifen Chen and Man-Ling Lee
    Citation: Journal of Cheminformatics 2015 7:11
    Content type: Software Published on:

  5. Wikipedia, the world’s largest and most popular encyclopedia is an indispensable source of chemistry information. It contains among others also entries for over 15,000 chemicals including metabolites, drugs, a...

    Authors: Peter Ertl, Luc Patiny, Thomas Sander, Christian Rufener and Michaël Zasso
    Citation: Journal of Cheminformatics 2015 7:10
    Content type: Software Published on:

  6. The current rise in the use of open lab notebook techniques means that there are an increasing number of scientists who make chemical information freely and openly available to the entire community as a series...

    Authors: Alex M Clark, Antony J Williams and Sean Ekins
    Citation: Journal of Cheminformatics 2015 7:9
    Content type: Research article Published on:

  7. Computational models based in Quantitative-Structure Activity Relationship (QSAR) methodologies are widely used tools for predicting the biological properties of new compounds. In many instances, such models a...

    Authors: Pau Carrió, Oriol López, Ferran Sanz and Manuel Pastor
    Citation: Journal of Cheminformatics 2015 7:8
    Content type: Software Published on:

  9. Volume of distribution is an important pharmacokinetic property that indicates the extent of a drug’s distribution in the body tissues. This paper addresses the problem of how to estimate the apparent volume o...

    Authors: Alex A Freitas, Kriti Limbu and Taravat Ghafourian
    Citation: Journal of Cheminformatics 2015 7:6
    Content type: Research article Published on:

  10. The rapid increase in the emergence of novel chemical substances presents a substantial demands for more sophisticated computational methodologies for drug discovery. In this study, the idea of Learning to Rank i...

    Authors: Wei Zhang, Lijuan Ji, Yanan Chen, Kailin Tang, Haiping Wang, Ruixin Zhu, Wei Jia, Zhiwei Cao and Qi Liu
    Citation: Journal of Cheminformatics 2015 7:5
    Content type: Research article Published on:

  11. The use of structural alerts to de-prioritize compounds with undesirable features as drug candidates has been gaining in popularity. Hundreds of molecular structural moieties have been proposed as structural a...

    Authors: Ruifeng Liu, Xueping Yu and Anders Wallqvist
    Citation: Journal of Cheminformatics 2015 7:4
    Content type: Research article Published on:

  13. Small chemical molecules regulate biological processes at the molecular level. Those molecules are often involved in causing or treating pathological states. Automatically identifying such molecules in biomedi...

    Authors: Anabel Usié, Joaquim Cruz, Jorge Comas, Francesc Solsona and Rui Alves
    Citation: Journal of Cheminformatics 2015 7(Suppl 1):S15
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  14. The functions of chemical compounds and drugs that affect biological processes and their particular effect on the onset and treatment of diseases have attracted increasing interest with the advancement of rese...

    Authors: Hong-Jie Dai, Po-Ting Lai, Yung-Chun Chang and Richard Tzong-Han Tsai
    Citation: Journal of Cheminformatics 2015 7(Suppl 1):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  15. Our approach to the BioCreative IV challenge of recognition and classification of drug names (CHEMDNER task) aimed at achieving high levels of precision by applying semantic similarity validation techniques to...

    Authors: Andre Lamurias, João D Ferreira and Francisco M Couto
    Citation: Journal of Cheminformatics 2015 7(Suppl 1):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  16. As we are witnessing a great interest in identifying and extracting chemical entities in academic articles, many approaches have been proposed to solve this problem. In this work we describe a probabilistic fr...

    Authors: Madian Khabsa and C Lee Giles
    Citation: Journal of Cheminformatics 2015 7(Suppl 1):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  17. In order to improve information access on chemical compounds and drugs (chemical entities) described in text repositories, it is very crucial to be able to identify chemical entity mentions (CEMs) automaticall...

    Authors: Shuo Xu, Xin An, Lijun Zhu, Yunliang Zhang and Haodong Zhang
    Citation: Journal of Cheminformatics 2015 7(Suppl 1):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  18. The past decade has seen an upsurge in the number of publications in chemistry. The ever-swelling volume of available documents makes it increasingly hard to extract relevant new information from such unstruct...

    Authors: Saber A Akhondi, Kristina M Hettne, Eelke van der Horst, Erik M van Mulligen and Jan A Kors
    Citation: Journal of Cheminformatics 2015 7(Suppl 1):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  19. Chemical and biomedical Named Entity Recognition (NER) is an essential prerequisite task before effective text mining can begin for biochemical-text data. Exploiting unlabeled text data to leverage system perf...

    Authors: Tsendsuren Munkhdalai, Meijing Li, Khuyagbaatar Batsuren, Hyeon Ah Park, Nak Hyeon Choi and Keun Ho Ryu
    Citation: Journal of Cheminformatics 2015 7(Suppl 1):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  20. Chemical compounds and drugs (together called chemical entities) embedded in scientific articles are crucial for many information extraction tasks in the biomedical domain. However, only a very limited number ...

    Authors: Buzhou Tang, Yudong Feng, Xiaolong Wang, Yonghui Wu, Yaoyun Zhang, Min Jiang, Jingqi Wang and Hua Xu
    Citation: Journal of Cheminformatics 2015 7(Suppl 1):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  21. The recognition of drugs and chemical entities in text is a very important task within the field of biomedical information extraction, given the rapid growth in the amount of published texts (scientific papers...

    Authors: David Campos, Sérgio Matos and José L Oliveira
    Citation: Journal of Cheminformatics 2015 7(Suppl 1):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  22. The development of robust methods for chemical named entity recognition, a challenging natural language processing task, was previously hindered by the lack of publicly available, large-scale, gold standard co...

    Authors: Riza Batista-Navarro, Rafal Rak and Sophia Ananiadou
    Citation: Journal of Cheminformatics 2015 7(Suppl 1):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  23. Chemical entity recognition has traditionally been performed by machine learning approaches. Here we describe an approach using grammars and dictionaries. This approach has the advantage that the entities foun...

    Authors: Daniel M Lowe and Roger A Sayle
    Citation: Journal of Cheminformatics 2015 7(Suppl 1):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  24. The chemical compound and drug name recognition plays an important role in chemical text mining, and it is the basis for automatic relation extraction and event identification in chemical information processin...

    Authors: Yanan Lu, Donghong Ji, Xiaoyuan Yao, Xiaomei Wei and Xiaohui Liang
    Citation: Journal of Cheminformatics 2015 7(Suppl 1):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  25. Chemical compounds and drugs are an important class of entities in biomedical research with great potential in a wide range of applications, including clinical medicine. Locating chemical named entities in the...

    Authors: Robert Leaman, Chih-Hsuan Wei and Zhiyong Lu
    Citation: Journal of Cheminformatics 2015 7(Suppl 1):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  26. The automatic extraction of chemical information from text requires the recognition of chemical entity mentions as one of its key steps. When developing supervised named entity recognition (NER) systems, the a...

    Authors: Martin Krallinger, Obdulia Rabal, Florian Leitner, Miguel Vazquez, David Salgado, Zhiyong Lu, Robert Leaman, Yanan Lu, Donghong Ji, Daniel M Lowe, Roger A Sayle, Riza Theresa Batista-Navarro, Rafal Rak, Torsten Huber, Tim Rocktäschel, Sérgio Matos…
    Citation: Journal of Cheminformatics 2015 7(Suppl 1):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  27. Natural language processing (NLP) and text mining technologies for the chemical domain (ChemNLP or chemical text mining) are key to improve the access and integration of information from unstructured data such as...

    Authors: Martin Krallinger, Florian Leitner, Obdulia Rabal, Miguel Vazquez, Julen Oyarzabal and Alfonso Valencia
    Citation: Journal of Cheminformatics 2015 7(Suppl 1):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 1

  29. Cyclooxygenases (COX) are present in the body in two isoforms, namely: COX-1, constitutively expressed, and COX-2, induced in physiopathological conditions such as cancer or chronic inflammation. The inhibitio...

    Authors: Isidro Cortes-Ciriano, Daniel S Murrell, Gerard JP van Westen, Andreas Bender and Thérèse E Malliavin
    Citation: Journal of Cheminformatics 2015 7:1
    Content type: Research Article Published on:

  30. QSAR is an established and powerful method for cheap in silico assessment of physicochemical properties and biological activities of chemical compounds. However, QSAR models are rather complex mathematical constr...

    Authors: Yurii Sushko, Sergii Novotarskyi, Robert Körner, Joachim Vogt, Ahmed Abdelaziz and Igor V Tetko
    Citation: Journal of Cheminformatics 2014 6:48
    Content type: Methodology Published on:

  31. Generally, QSAR modelling requires both model selection and validation since there is no a priori knowledge about the optimal QSAR model. Prediction errors (PE) are frequently used to select and to assess the mod...

    Authors: Désirée Baumann and Knut Baumann
    Citation: Journal of Cheminformatics 2014 6:47
    Content type: Research article Published on:

  32. Methods that provide a measure of chemical similarity are strongly relevant in several fields of chemoinformatics as they allow to predict the molecular behavior and fate of structurally close compounds. One c...

    Authors: Matteo Floris, Alberto Manganaro, Orazio Nicolotti, Ricardo Medda, Giuseppe Felice Mangiatordi and Emilio Benfenati
    Citation: Journal of Cheminformatics 2014 6:39
    Content type: Research article Published on:

  33. Tuberculosis (TB) is the second leading cause of death from a single infectious organism, demanding attention towards discovery of novel anti-tubercular compounds. Natural products or their derivatives have pr...

    Authors: Arun Sharma, Prasun Dutta, Maneesh Sharma, Neeraj Kumar Rajput, Bhavna Dodiya, John J Georrge, Trupti Kholia and Anshu Bhardwaj
    Citation: Journal of Cheminformatics 2014 6:46
    Content type: Database Published on:

  34. Mesoscopic simulation studies the structure, dynamics and properties of large molecular ensembles with millions of atoms: Its basic interacting units (beads) are no longer the nuclei and electrons of quantum c...

    Authors: Andreas Truszkowski, Mirco Daniel, Hubert Kuhn, Stefan Neumann, Christoph Steinbeck, Achim Zielesny and Matthias Epple
    Citation: Journal of Cheminformatics 2014 6:45
    Content type: Methodology Published on:

  35. Sound statistical validation is important to evaluate and compare the overall performance of (Q)SAR models. However, classical validation does not support the user in better understanding the properties of the...

    Authors: Martin Gütlein, Andreas Karwath and Stefan Kramer
    Citation: Journal of Cheminformatics 2014 6:41
    Content type: Software Published on:

  36. Hierarchical clustering is an exploratory data analysis method that reveals the groups (clusters) of similar objects. The result of the hierarchical clustering is a tree structure called dendrogram that shows ...

    Authors: Ctibor Škuta, Petr Bartůněk and Daniel Svozil
    Citation: Journal of Cheminformatics 2014 6:44
    Content type: Software Published on:

  37. The design of chemical libraries, an early step in agrochemical discovery programs, is frequently addressed by means of qualitative physicochemical and/or topological rule-based methods. The aim of this study ...

    Authors: Sorin Avram, Simona Funar-Timofei, Ana Borota, Sridhar Rao Chennamaneni, Anil Kumar Manchala and Sorel Muresan
    Citation: Journal of Cheminformatics 2014 6:42
    Content type: Research article Published on:

  38. UniChem is a low-maintenance, fast and freely available compound identifier mapping service, recently made available on the Internet. Until now, the criterion of molecular equivalence within UniChem has been o...

    Authors: Jon Chambers, Mark Davies, Anna Gaulton, George Papadatos, Anne Hersey and John P Overington
    Citation: Journal of Cheminformatics 2014 6:43
    Content type: Database Published on:

  39. The large increase in the number of scientific publications has fuelled a need for semi- and fully automated text mining approaches in order to assist in the triage process, both for individual scientists and ...

    Authors: George Papadatos, Gerard JP van Westen, Samuel Croset, Rita Santos, Simone Trubian and John P Overington
    Citation: Journal of Cheminformatics 2014 6:40
    Content type: Software Published on:

  40. We recently developed a freely available mobile app (TB Mobile) for both iOS and Android platforms that displays Mycobacterium tuberculosis (Mtb) active molecule structures and their targets with links to associa...

    Authors: Alex M Clark, Malabika Sarker and Sean Ekins
    Citation: Journal of Cheminformatics 2014 6:38
    Content type: Research article Published on:

  42. Proteochemometrics (PCM) is an approach for bioactivity predictive modeling which models the relationship between protein and chemical information. Gaussian Processes (GP), based on Bayesian inference, provide...

    Authors: Isidro Cortes-Ciriano, Gerard JP van Westen, Eelke Bart Lenselink, Daniel S Murrell, Andreas Bender and Thérèse Malliavin
    Citation: Journal of Cheminformatics 2014 6:35
    Content type: Research article Published on:

  43. A foundational library called MORT (Molecular Objects and Relevant Templates) for the development of new software packages and tools employed in computational biology and computer-aided drug design (CADD) is d...

    Authors: Qian Zhang, Wei Zhang, Youyong Li, Junmei Wang, Jian Zhang and Tingjun Hou
    Citation: Journal of Cheminformatics 2014 6:36
    Content type: Software Published on:

  44. Quantitative structure-activity (QSAR) models have enormous potential for reducing drug discovery and development costs as well as the need for animal testing. Great strides have been made in estimating their ...

    Authors: Robert D Clark, Wenkel Liang, Adam C Lee, Michael S Lawless, Robert Fraczkiewicz and Marvin Waldman
    Citation: Journal of Cheminformatics 2014 6:34
    Content type: Research article Published on:

  45. Ligand-based in silico target fishing can be used to identify the potential interacting target of bioactive ligands, which is useful for understanding the polypharmacology and safety profile of existing drugs. Th...

    Authors: Xian Liu, Yuan Xu, Shanshan Li, Yulan Wang, Jianlong Peng, Cheng Luo, Xiaomin Luo, Mingyue Zheng, Kaixian Chen and Hualiang Jiang
    Citation: Journal of Cheminformatics 2014 6:33
    Content type: Research article Published on:

  49. The prediction of sites and products of metabolism in xenobiotic compounds is key to the development of new chemical entities, where screening potential metabolites for toxicity or unwanted side-effects is of ...

    Authors: Jonathan D Tyzack, Hamse Y Mussa, Mark J Williamson, Johannes Kirchmair and Robert C Glen
    Citation: Journal of Cheminformatics 2014 6:29
    Content type: Research article Published on:

  50. The progress in computer-aided drug design (CADD) approaches over the past decades accelerated the early-stage pharmaceutical research. Many powerful standalone tools for CADD have been developed in academia. ...

    Authors: Xia Wang, Haipeng Chen, Feng Yang, Jiayu Gong, Shiliang Li, Jianfeng Pei, Xiaofeng Liu, Hualiang Jiang, Luhua Lai and Honglin Li
    Citation: Journal of Cheminformatics 2014 6:28
    Content type: Methodology Published on:
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