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  1. Software

    Geomfinder: a multi-feature identifier of similar three-dimensional protein patterns: a ligand-independent approach

    Since the structure of proteins is more conserved than the sequence, the identification of conserved three-dimensional (3D) patterns among a set of proteins, can be important for protein function prediction, p...

    Gabriel Núñez-Vivanco, Alejandro Valdés-Jiménez, Felipe Besoaín and Miguel Reyes-Parada

    Journal of Cheminformatics 2016 8:19

    Published on: 18 April 2016

  2. Software

    Supercell program: a combinatorial structure-generation approach for the local-level modeling of atomic substitutions and partial occupancies in crystals

    Disordered compounds are crucially important for fundamental science and industrial applications. Yet most available methods to explore solid-state material properties require ideal periodicity, which, strictl...

    Kirill Okhotnikov, Thibault Charpentier and Sylvian Cadars

    Journal of Cheminformatics 2016 8:17

    Published on: 31 March 2016

  3. Research article

    Impact of similarity threshold on the topology of molecular similarity networks and clustering outcomes

    Complex network theory based methods and the emergence of “Big Data” have reshaped the terrain of investigating structure-activity relationships of molecules. This change gave rise to new methods which need to...

    Gergely Zahoránszky-Kőhalmi, Cristian G. Bologa and Tudor I. Oprea

    Journal of Cheminformatics 2016 8:16

    Published on: 30 March 2016

    The Erratum to this article has been published in Journal of Cheminformatics 2016 8:28

  4. Research article

    DASPfind: new efficient method to predict drug–target interactions

    Identification of novel drug–target interactions (DTIs) is important for drug discovery. Experimental determination of such DTIs is costly and time consuming, hence it necessitates the development of efficient...

    Wail Ba-alawi, Othman Soufan, Magbubah Essack, Panos Kalnis and Vladimir B. Bajic

    Journal of Cheminformatics 2016 8:15

    Published on: 16 March 2016

  5. Software

    libChEBI: an API for accessing the ChEBI database

    ChEBI is a database and ontology of chemical entities of biological interest. It is widely used as a source of identifiers to facilitate unambiguous reference to chemical entities within biological models, dat...

    Neil Swainston, Janna Hastings, Adriano Dekker, Venkatesh Muthukrishnan, John May, Christoph Steinbeck and Pedro Mendes

    Journal of Cheminformatics 2016 8:11

    Published on: 1 March 2016

  6. Research article

    Examining the predictive accuracy of the novel 3D N-linear algebraic molecular codifications on benchmark datasets

    Recently, novel 3D alignment-free molecular descriptors (also known as QuBiLS-MIDAS) based on two-linear, three-linear and four-linear algebraic forms have been introduced. These descriptors codify chemical in...

    César R. García-Jacas, Ernesto Contreras-Torres, Yovani Marrero-Ponce, Mario Pupo-Meriño, Stephen J. Barigye and Lisset Cabrera-Leyva

    Journal of Cheminformatics 2016 8:10

    Published on: 25 February 2016

  7. Research article

    Effects of using structured templates for recalling chemistry experiments

    The way that we recall information is dependent upon both the knowledge in our memories and the conditions under which we recall the information. Electronic Laboratory Notebooks can provide a structured interf...

    Cerys Willoughby, Thomas A. Logothetis and Jeremy G. Frey

    Journal of Cheminformatics 2016 8:9

    Published on: 19 February 2016

  8. Research article

    Selectivity profiling of BCRP versus P-gp inhibition: from automated collection of polypharmacology data to multi-label learning

    The human ATP binding cassette transporters Breast Cancer Resistance Protein (BCRP) and Multidrug Resistance Protein 1 (P-gp) are co-expressed in many tissues and barriers, especially at the blood–brain barrie...

    Floriane Montanari, Barbara Zdrazil, Daniela Digles and Gerhard F. Ecker

    Journal of Cheminformatics 2016 8:7

    Published on: 4 February 2016

  9. Research article

    ADMET evaluation in drug discovery: 15. Accurate prediction of rat oral acute toxicity using relevance vector machine and consensus modeling

    Determination of acute toxicity, expressed as median lethal dose (LD50), is one of the most important steps in drug discovery pipeline. Because in vivo assays for oral acute toxicity in mammals are time-consumin...

    Tailong Lei, Youyong Li, Yunlong Song, Dan Li, Huiyong Sun and Tingjun Hou

    Journal of Cheminformatics 2016 8:6

    Published on: 1 February 2016

  10. Research Article

    Fragmentation trees reloaded

    Untargeted metabolomics commonly uses liquid chromatography mass spectrometry to measure abundances of metabolites; subsequent tandem mass spectrometry is used to derive information about individual compounds....

    Sebastian Böcker and Kai Dührkop

    Journal of Cheminformatics 2016 8:5

    Published on: 1 February 2016

  11. Software

    MetFrag relaunched: incorporating strategies beyond in silico fragmentation

    The in silico fragmenter MetFrag, launched in 2010, was one of the first approaches combining compound database searching and fragmentation prediction for small molecule identification from tandem mass spectromet...

    Christoph Ruttkies, Emma L. Schymanski, Sebastian Wolf, Juliane Hollender and Steffen Neumann

    Journal of Cheminformatics 2016 8:3

    Published on: 29 January 2016

  12. Research article

    How frequently do clusters occur in hierarchical clustering analysis? A graph theoretical approach to studying ties in proximity

    Hierarchical cluster analysis (HCA) is a widely used classificatory technique in many areas of scientific knowledge. Applications usually yield a dendrogram from an HCA run over a given data set, using a group...

    Wilmer Leal, Eugenio J. Llanos, Guillermo Restrepo, Carlos F. Suárez and Manuel Elkin Patarroyo

    Journal of Cheminformatics 2016 8:4

    Published on: 25 January 2016

  13. Research Article

    The development of models to predict melting and pyrolysis point data associated with several hundred thousand compounds mined from PATENTS

    Melting point (MP) is an important property in regards to the solubility of chemical compounds. Its prediction from chemical structure remains a highly challenging task for quantitative structure–activity rel...

    Igor V. Tetko, Daniel M. Lowe and Antony J. Williams

    Journal of Cheminformatics 2016 8:2

    Published on: 22 January 2016

  14. Research article

    vSDC: a method to improve early recognition in virtual screening when limited experimental resources are available

    In drug design, one may be confronted to the problem of finding hits for targets for which no small inhibiting molecules are known and only low-throughput experiments are available (like ITC or NMR studies), t...

    Ludovic Chaput, Juan Martinez-Sanz, Eric Quiniou, Pascal Rigolet, Nicolas Saettel and Liliane Mouawad

    Journal of Cheminformatics 2016 8:1

    Published on: 18 January 2016

  15. Research article

    Smiles2Monomers: a link between chemical and biological structures for polymers

    The monomeric composition of polymers is powerful for structure comparison and synthetic biology, among others. Many databases give access to the atomic structure of compounds but the monomeric structure of po...

    Yoann Dufresne, Laurent Noé, Valérie Leclère and Maude Pupin

    Journal of Cheminformatics 2015 7:62

    Published on: 29 December 2015

  16. Software

    ChemDes: an integrated web-based platform for molecular descriptor and fingerprint computation

    Molecular descriptors and fingerprints have been routinely used in QSAR/SAR analysis, virtual drug screening, compound search/ranking, drug ADME/T prediction and other drug discovery processes. Since the calc...

    Jie Dong, Dong-Sheng Cao, Hong-Yu Miao, Shao Liu, Bai-Chuan Deng, Yong-Huan Yun, Ning-Ning Wang, Ai-Ping Lu, Wen-Bin Zeng and Alex F. Chen

    Journal of Cheminformatics 2015 7:60

    Published on: 9 December 2015

  17. Research article

    High-quality and universal empirical atomic charges for chemoinformatics applications

    Partial atomic charges describe the distribution of electron density in a molecule and therefore provide clues to the chemical behaviour of molecules. Recently, these charges have become popular in chemoinform...

    Stanislav Geidl, Tomáš Bouchal, Tomáš Raček, Radka Svobodová Vařeková, Václav Hejret, Aleš Křenek, Ruben Abagyan and Jaroslav Koča

    Journal of Cheminformatics 2015 7:59

    Published on: 2 December 2015

  18. Commentary

    A note on utilising binary features as ligand descriptors

    It is common in cheminformatics to represent the properties of a ligand as a string of 1’s and 0’s, with the intention of elucidating, inter alia, the relationship between the chemical structure of a ligand and i...

    Hamse Y. Mussa, John B. O. Mitchell and Robert C. Glen

    Journal of Cheminformatics 2015 7:58

    Published on: 1 December 2015

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