Volume 9; Issue 1

Journal of Cheminformatics

Volume 9; Issue 1

1

Mapping and classifying molecules from a high-throughput structural database

De, Sandip, Musil, Felix, Ingram, Teresa, Baldauf, Carsten, Ceriotti, Michele

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 15.45 MB

english, 2017

2

A novel descriptor based on atom-pair properties

Kuroda, Masataka

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.80 MB

english, 2017

3

NPCARE: database of natural products and fractional extracts for cancer regulation

Choi, Hwanho, Cho, Sun Young, Pak, Ho Jeong, Kim, Youngsoo, Choi, Jung-yun, Lee, Yoon Jae, Gong, Byung Hee, Kang, Yeon Seok, Han, Taehoon, Choi, Geunbae, Cho, Yeeun, Lee, Soomin, Ryoo, Dekwoo, Park, H

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 4.57 MB

english, 2017

4

S2RSLDB: a comprehensive manually curated, internet-accessible database of the sigma-2 receptor selective ligands

Nastasi, Giovanni, Miceli, Carla, Pittalà, Valeria, Modica, Maria N., Prezzavento, Orazio, Romeo, Giuseppe, Rescifina, Antonio, Marrazzo, Agostino, Amata, Emanuele

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.51 MB

english, 2017

5

Adverse drug reactions triggered by the common HLA-B*57:01 variant: a molecular docking study

Van Den Driessche, George, Fourches, Denis

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 5.79 MB

english, 2017

6

Database fingerprint (DFP): an approach to represent molecular databases

Fernández-de Gortari, Eli, García-Jacas, César R., Martinez-Mayorga, Karina, Medina-Franco, José L.

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 3.97 MB

english, 2017

7

SkinSensDB: a curated database for skin sensitization assays

Wang, Chia-Chi, Lin, Ying-Chi, Wang, Shan-Shan, Shih, Chieh, Lin, Yi-Hui, Tung, Chun-Wei

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.10 MB

english, 2017

8

Comprehensive identification of sphingolipid species by in silico retention time and tandem mass spectral library

Tsugawa, Hiroshi, Ikeda, Kazutaka, Tanaka, Wataru, Senoo, Yuya, Arita, Makoto, Arita, Masanori

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.52 MB

english, 2017

9

Analysis of drug–endogenous human metabolite similarities in terms of their maximum common substructures

O’Hagan, Steve, Kell, Douglas B.

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 5.96 MB

english, 2017

10

ExCAPE-DB: an integrated large scale dataset facilitating Big Data analysis in chemogenomics

Sun, Jiangming, Jeliazkova, Nina, Chupakin, Vladimir, Golib-Dzib, Jose-Felipe, Engkvist, Ola, Carlsson, Lars, Wegner, Jörg, Ceulemans, Hugo, Georgiev, Ivan, Jeliazkov, Vedrin, Kochev, Nikolay, Ashby,

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 2.28 MB

english, 2017

11

The comparison of automated clustering algorithms for resampling representative conformer ensembles with RMSD matrix

Kim, Hyoungrae, Jang, Cheongyun, Yadav, Dharmendra K., Kim, Mi-hyun

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 4.83 MB

english, 2017

12

The polypharmacology browser: a web-based multi-fingerprint target prediction tool using ChEMBL bioactivity data

Awale, Mahendra, Reymond, Jean-Louis

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.64 MB

english, 2017

13

Comparative analyses of structural features and scaffold diversity for purchasable compound libraries

Shang, Jun, Sun, Huiyong, Liu, Hui, Chen, Fu, Tian, Sheng, Pan, Peichen, Li, Dan, Kong, Dexin, Hou, Tingjun

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 2.93 MB

english, 2017

14

Large-scale virtual screening on public cloud resources with Apache Spark

Capuccini, Marco, Ahmed, Laeeq, Schaal, Wesley, Laure, Erwin, Spjuth, Ola

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.29 MB

english, 2017

15

Predicting drug–drug interactions through drug structural similarities and interaction networks incorporating pharmacokinetics and pharmacodynamics knowledge

Takako Takeda,Ming Hao,Tiejun Cheng,Stephen H. Bryant…

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.81 MB

english, 2017

16

The power metric: a new statistically robust enrichment-type metric for virtual screening applications with early recovery capability

Lopes, Julio Cesar Dias, dos Santos, Fábio Mendes, Martins-José, Andrelly, Augustyns, Koen, De Winter, Hans

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 2.24 MB

english, 2017

17

A possible extension to the RInChI as a means of providing machine readable process data

Jacob, Philipp-Maximilian, Lan, Tian, Goodman, Jonathan M., Lapkin, Alexei A.

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.20 MB

english, 2017

18

Scaffold Hunter: a comprehensive visual analytics framework for drug discovery

Schäfer, Till, Kriege, Nils, Humbeck, Lina, Klein, Karsten, Koch, Oliver, Mutzel, Petra

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 8.36 MB

english, 2017

19

Searching for bioactive conformations of drug-like ligands with current force fields: how good are we?

Gürsoy, Oya, Smieško, Martin

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 2.09 MB

english, 2017

20

Electronic lab notebooks: can they replace paper?

Kanza, Samantha, Willoughby, Cerys, Gibbins, Nicholas, Whitby, Richard, Frey, Jeremy Graham, Erjavec, Jana, Zupančič, Klemen, Hren, Matjaž, Kovač, Katarina

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 2.63 MB

english, 2017

21

QuBiLS-MAS, open source multi-platform software for atom- and bond-based topological (2D) and chiral (2.5D) algebraic molecular descriptors computations

Valdés-Martiní, José R., Marrero-Ponce, Yovani, García-Jacas, César R., Martinez-Mayorga, Karina, Barigye, Stephen J., Vaz d‘Almeida, Yasser Silveira, Pham-The, Hai, Pérez-Giménez, Facundo, Morell, Ca

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 3.95 MB

english, 2017

22

A metadata-driven approach to data repository design

Matthew J. Harvey,Andrew McLean,Henry S. Rzepa

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 2.10 MB

english, 2017

23

Automatic procedure for generating symmetry adapted wavefunctions

Marcus Johansson,Valera Veryazov

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.47 MB

english, 2017

24

Technical implications of new IUPAC elements in cheminformatics

John W. Mayfield,Roger A. Sayle

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 752 KB

english, 2017

25

Nontargeted homologue series extraction from hyphenated high resolution mass spectrometry data

Martin Loos,Heinz Singer

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 2.70 MB

english, 2017

26

Modeling framework for isotopic labeling of heteronuclear moieties

Mark I. Borkum,Patrick N. Reardon,Ronald C. Taylor…

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.44 MB

english, 2017

27

Nonpher: computational method for design of hard-to-synthesize structures

Milan Voršilák,Daniel Svozil

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.20 MB

english, 2017

28

Critical Assessment of Small Molecule Identification 2016: automated methods

Emma L. Schymanski,Christoph Ruttkies,Martin Krauss…

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.90 MB

english, 2017

29

SimBoost: a read-across approach for predicting drug–target binding affinities using gradient boosting machines

Tong He,Marten Heidemeyer,Fuqiang Ban,Artem Cherkasov…

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 2.35 MB

english, 2017

30

Assessment of the significance of patent-derived information for the early identification of compound–target interaction hypotheses

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.09 MB

english, 2017

31

ChemSAR: an online pipelining platform for molecular SAR modeling

Jie Dong,Zhi-Jiang Yao,Min-Feng Zhu,Ning-Ning Wang,Ben Lu…

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.71 MB

english, 2017

32

Helping to improve the practice of cheminformatics

Rajarshi Guha,Egon Willighagen

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 912 KB

english, 2017

33

Comprehensive comparison of in silico MS/MS fragmentation tools of the CASMI contest: database boosting is needed to achieve 93% accuracy

Ivana Blaženović,Tobias Kind,Hrvoje Torbašinović…

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.40 MB

english, 2017

34

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

Egon L. Willighagen,John W. Mayfield,Jonathan Alvarsson…

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 2.30 MB

english, 2017

35

Erratum to: ExCAPE-DB: an integrated large scale dataset facilitating Big Data analysis in chemogenomics

Jiangming Sun,Nina Jeliazkova,Vladimir Chupakhin…

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 685 KB

english, 2017

36

Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D

German A. Preciat Gonzalez,Lemmer R. P. El Assal…

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 2.89 MB

english, 2017

37

RANdom SAmple Consensus (RANSAC) algorithm for material-informatics: application to photovoltaic solar cells

Omer Kaspi,Abraham Yosipof,Hanoch Senderowitz

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 2.14 MB

english, 2017

38

An algorithm to identify functional groups in organic molecules

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 3.01 MB

english, 2017

39

Efficient conformational sampling and weak scoring in docking programs? Strategy of the wisdom of crowds

Ludovic Chaput,Liliane Mouawad

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.69 MB

english, 2017

40

chemalot and chemalot_knime: Command line programs as workflow tools for drug discovery

Man-Ling Lee,Ignacio Aliagas,Jianwen A. Feng…

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 2.68 MB

english, 2017

41

Deep-learning: investigating deep neural networks hyper-parameters and comparison of performance to shallow methods for modeling bioactivity data

Alexios Koutsoukas,Keith J. Monaghan,Xiaoli Li,Jun Huan

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.27 MB

english, 2017

42

Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set

Lenselink, Eelke B., ten Dijke, Niels, Bongers, Brandon, Papadatos, George, van Vlijmen, Herman W. T., Kowalczyk, Wojtek, IJzerman, Adriaan P., van Westen, Gerard J. P.

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.34 MB

english, 2017

43

An efficient computer-aided structural elucidation strategy for mixtures using an iterative dynamic programming algorithm

Su, Bo-Han, Shen, Meng-Yu, Harn, Yeu-Chern, Wang, San-Yuan, Schurz, Alioune, Lin, Chieh, Lin, Olivia A., Tseng, Yufeng J.

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.95 MB

english, 2017

44

G.A.M.E.: GPU-accelerated mixture elucidator

Schurz, Alioune, Su, Bo-Han, Tu, Yi-Shu, Lu, Tony Tsung-Yu, Lin, Olivia A., Tseng, Yufeng J.

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.20 MB

english, 2017

45

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application

Hanwell, Marcus D., de Jong, Wibe A., Harris, Christopher J.

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.12 MB

english, 2017

46

Efficiency of different measures for defining the applicability domain of classification models

Klingspohn, Waldemar, Mathea, Miriam, ter Laak, Antonius, Heinrich, Nikolaus, Baumann, Knut

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.70 MB

english, 2017

47

Molecular de-novo design through deep reinforcement learning

Olivecrona, Marcus, Blaschke, Thomas, Engkvist, Ola, Chen, Hongming

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.52 MB

english, 2017

48

A posteriori metadata from automated provenance tracking: integration of AiiDA and TCOD

Merkys, Andrius, Mounet, Nicolas, Cepellotti, Andrea, Marzari, Nicola, Gražulis, Saulius, Pizzi, Giovanni

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.31 MB

english, 2017

49

Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm

Skinnider, Michael A., Dejong, Chris A., Franczak, Brian C., McNicholas, Paul D., Magarvey, Nathan A.

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.02 MB

english, 2017

50

A review of parameters and heuristics for guiding metabolic pathfinding

Kim, Sarah M., Peña, Matthew I., Moll, Mark, Bennett, George N., Kavraki, Lydia E.

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.72 MB

english, 2017

51

Data driven polypharmacological drug design for lung cancer: analyses for targeting ALK, MET, and EGFR

Narayanan, Dilip, Gani, Osman A. B. S. M., Gruber, Franz X. E., Engh, Richard A.

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 4.52 MB

english, 2017

52

Erratum to: The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

Willighagen, Egon L., Mayfield, John W., Alvarsson, Jonathan, Berg, Arvid, Carlsson, Lars, Jeliazkova, Nina, Kuhn, Stefan, Pluskal, Tomáš, Rojas-Chertó, Miquel, Spjuth, Ola, Torrance, Gilleain, Evelo,

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 700 KB

english, 2017

53

Computational methods using weighed-extreme learning machine to predict protein self-interactions with protein evolutionary information

An, Ji-Yong, Zhang, Lei, Zhou, Yong, Zhao, Yu-Jun, Wang, Da-Fu

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.16 MB

english, 2017

54

Beware of ligand efficiency (LE): understanding LE data in modeling structure-activity and structure-economy relationships

Polanski, Jaroslaw, Tkocz, Aleksandra, Kucia, Urszula

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.94 MB

english, 2017

55

Scoria: a Python module for manipulating 3D molecular data

Ropp, Patrick, Friedman, Aaron, Durrant, Jacob D.

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.27 MB

english, 2017

56

Chemotion ELN: an Open Source electronic lab notebook for chemists in academia

Tremouilhac, Pierre, Nguyen, An, Huang, Yu-Chieh, Kotov, Serhii, Lütjohann, Dominic Sebastian, Hübsch, Florian, Jung, Nicole, Bräse, Stefan

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 2.20 MB

english, 2017

57

eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations

Capoferri, Luigi, van Dijk, Marc, Rustenburg, Ariën S., Wassenaar, Tsjerk A., Kooi, Derk P., Rifai, Eko A., Vermeulen, Nico P. E., Geerke, Daan P.

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 2.25 MB

english, 2017

58

Efficient conformational ensemble generation of protein-bound peptides

Yan, Yumeng, Zhang, Di, Huang, Sheng-You

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.45 MB

english, 2017

59

The CompTox Chemistry Dashboard: a community data resource for environmental chemistry

Williams, Antony J., Grulke, Christopher M., Edwards, Jeff, McEachran, Andrew D., Mansouri, Kamel, Baker, Nancy C., Patlewicz, Grace, Shah, Imran, Wambaugh, John F., Judson, Richard S., Richard, Ann M

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 2.95 MB

english, 2017

60

Consensus queries in ligand-based virtual screening experiments

Berenger, Francois, Vu, Oanh, Meiler, Jens

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.50 MB

english, 2017

61

Computer-aided design of multi-target ligands at A1R, A2AR and PDE10A, key proteins in neurodegenerative diseases

Kalash, Leen, Val, Cristina, Azuaje, Jhonny, Loza, María I., Svensson, Fredrik, Zoufir, Azedine, Mervin, Lewis, Ladds, Graham, Brea, José, Glen, Robert, Sotelo, Eddy, Bender, Andreas

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.36 MB

english, 2017

62

Can human experts predict solubility better than computers?

Boobier, Samuel, Osbourn, Anne, Mitchell, John B. O.

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.04 MB

english, 2017

63

BoBER: web interface to the base of bioisosterically exchangeable replacements

Lešnik, Samo, Škrlj, Blaž, Eržen, Nika, Bren, Urban, Gobec, Stanislav, Konc, Janez, Janežič, Dušanka

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.57 MB

english, 2017

64

Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0

Koch, Mathilde, Duigou, Thomas, Carbonell, Pablo, Faulon, Jean-Loup

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 2.44 MB

english, 2017

65

HawkRank: a new scoring function for protein–protein docking based on weighted energy terms

Feng, Ting, Chen, Fu, Kang, Yu, Sun, Huiyong, Liu, Hui, Li, Dan, Zhu, Feng, Hou, Tingjun

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 2.14 MB

english, 2017

66

Systematic exploration of multiple drug binding sites

Bálint, Mónika, Jeszenői, Norbert, Horváth, István, van der Spoel, David, Hetényi, Csaba

Journal:

Journal of Cheminformatics

Year:

2017

Language:

english

File:

PDF, 1.77 MB

english, 2017

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