Volume 10; Issue 1

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Journal of Cheminformatics
Volume 10; Issue 1

Journal of Cheminformatics

Volume 10; Issue 1

1

An automated framework for QSAR model building

Kausar, Samina, Falcao, Andre O.

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 2.04 MB

english, 2018

2

Automated reaction database and reaction network analysis: extraction of reaction templates using cheminformatics

Plehiers, Pieter P., Marin, Guy B., Stevens, Christian V., Van Geem, Kevin M.

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 2.34 MB

english, 2018

3

3D-QSAR study of steroidal and azaheterocyclic human aromatase inhibitors using quantitative profile of protein–ligand interactions

Lee, Sehan, Barron, Mace G.

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.36 MB

english, 2018

4

The dye-sensitized solar cell database

Venkatraman, Vishwesh, Raju, Rajesh, Oikonomopoulos, Solon P., Alsberg, Bjørn K.

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.48 MB

english, 2018

5

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

Šícho, M., Voršilák, M., Svozil, D.

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 907 KB

english, 2018

6

Finding the molecular scaffold of nuclear receptor inhibitors through high-throughput screening based on proteochemometric modelling

Qiu, Tianyi, Wu, Dingfeng, Qiu, Jingxuan, Cao, Zhiwei

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.57 MB

english, 2018

7

Key features and updates for Origin 2018

Moberly, James G., Bernards, Matthew T., Waynant, Kristopher V.

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 644 KB

english, 2018

8

Maximizing gain in high-throughput screening using conformal prediction

Svensson, Fredrik, Afzal, Avid M., Norinder, Ulf, Bender, Andreas

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.25 MB

english, 2018

9

Two inhibitors of yeast plasma membrane ATPase 1 (ScPma1p): toward the development of novel antifungal therapies

Ottilie, Sabine, Goldgof, Gregory M., Cheung, Andrea L., Walker, Jennifer L., Vigil, Edgar, Allen, Kenneth E., Antonova-Koch, Yevgeniya, Slayman, Carolyn W., Suzuki, Yo, Durrant, Jacob D.

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.09 MB

english, 2018

10

OPERA models for predicting physicochemical properties and environmental fate endpoints

Mansouri, Kamel, Grulke, Chris M., Judson, Richard S., Williams, Antony J.

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.81 MB

english, 2018

11

Efficient iterative virtual screening with Apache Spark and conformal prediction

Ahmed, Laeeq, Georgiev, Valentin, Capuccini, Marco, Toor, Salman, Schaal, Wesley, Laure, Erwin, Spjuth, Ola

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.08 MB

english, 2018

12

PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions

Dong, Jie, Yao, Zhi-Jiang, Zhang, Lin, Luo, Feijun, Lin, Qinlu, Lu, Ai-Ping, Chen, Alex F., Cao, Dong-Sheng

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.35 MB

english, 2018

13

Finding the K best synthesis plans

Fagerberg, Rolf, Flamm, Christoph, Kianian, Rojin, Merkle, Daniel, Stadler, Peter F.

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.85 MB

english, 2018

14

KRDS: a web server for evaluating drug resistance mutations in kinases by molecular docking

Lee, Aeri, Hong, Seungpyo, Kim, Dongsup

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.57 MB

english, 2018

15

A confidence predictor for logD using conformal regression and a support-vector machine

Lapins, Maris, Arvidsson, Staffan, Lampa, Samuel, Berg, Arvid, Schaal, Wesley, Alvarsson, Jonathan, Spjuth, Ola

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.59 MB

english, 2018

16

Reply to the comment made by Šicho, Vorśilák and Svozil on ‘The Power metric: a new statistically robust enrichment-type metric for virtual screening applications with early recovery capability’

De Winter, Hans, Lopes, Julio Cesar Dias

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 850 KB

english, 2018

17

Spectrophores as one-dimensional descriptors calculated from three-dimensional atomic properties: applications ranging from scaffold hopping to multi-target virtual screening

Gladysz, Rafaela, Dos Santos, Fabio Mendes, Langenaeker, Wilfried, Thijs, Gert, Augustyns, Koen, De Winter, Hans

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 2.32 MB

english, 2018

18

HIVprotI: an integrated web based platform for prediction and design of HIV proteins inhibitors

Qureshi, Abid, Rajput, Akanksha, Kaur, Gazaldeep, Kumar, Manoj

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 2.39 MB

english, 2018

19

Adverse drug reactions triggered by the common HLA-B*57:01 variant: virtual screening of DrugBank using 3D molecular docking

Van Den Driessche, George, Fourches, Denis

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 3.99 MB

english, 2018

20

Mordred: a molecular descriptor calculator

Moriwaki, Hirotomo, Tian, Yu-Shi, Kawashita, Norihito, Takagi, Tatsuya

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.43 MB

english, 2018

21

International chemical identifier for reactions (RInChI)

Grethe, Guenter, Blanke, Gerd, Kraut, Hans, Goodman, Jonathan M.

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.26 MB

english, 2018

22

Sachem: a chemical cartridge for high-performance substructure search

Kratochvíl, Miroslav, Vondrášek, Jiří, Galgonek, Jakub

Journal:

Journal of Cheminformatics

Year:

2018

File:

PDF, 1.48 MB

2018

23

Inferring potential small molecule–miRNA association based on triple layer heterogeneous network

Qu, Jia, Chen, Xing, Sun, Ya-Zhou, Li, Jian-Qiang, Ming, Zhong

Journal:

Journal of Cheminformatics

Year:

2018

File:

PDF, 1.91 MB

2018

24

PubChem chemical structure standardization

Hähnke, Volker D., Kim, Sunghwan, Bolton, Evan E.

Journal:

Journal of Cheminformatics

Year:

2018

File:

PDF, 8.10 MB

2018

25

ADMETlab: a platform for systematic ADMET evaluation based on a comprehensively collected ADMET database

Dong, Jie, Wang, Ning-Ning, Yao, Zhi-Jiang, Zhang, Lin, Cheng, Yan, Ouyang, Defang, Lu, Ai-Ping, Cao, Dong-Sheng

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.06 MB

english, 2018

26

Sachem: a chemical cartridge for high-performance substructure search

Kratochvíl, Miroslav, Vondrášek, Jiří, Galgonek, Jakub

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.48 MB

english, 2018

27

Inferring potential small molecule–miRNA association based on triple layer heterogeneous network

Qu, Jia, Chen, Xing, Sun, Ya-Zhou, Li, Jian-Qiang, Ming, Zhong

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.91 MB

english, 2018

28

PubChem chemical structure standardization

Hähnke, Volker D., Kim, Sunghwan, Bolton, Evan E.

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 8.10 MB

english, 2018

29

Jdpd: an open java simulation kernel for molecular fragment dissipative particle dynamics

van den Broek, Karina, Kuhn, Hubert, Zielesny, Achim

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.13 MB

english, 2018

30

Molecular generative model based on conditional variational autoencoder for de novo molecular design

Lim, Jaechang, Ryu, Seongok, Kim, Jin Woo, Kim, Woo Youn

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.39 MB

english, 2018

31

Predictive classification models and targets identification for betulin derivatives as Leishmania donovani inhibitors

Zhang, Yuezhou, Xhaard, Henri, Ghemtio, Leo

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 2.13 MB

english, 2018

32

Using SMILES strings for the description of chemical connectivity in the Crystallography Open Database

Quirós, Miguel, Gražulis, Saulius, Girdzijauskaitė, Saulė, Merkys, Andrius, Vaitkus, Antanas

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.56 MB

english, 2018

33

Effect of missing data on multitask prediction methods

de la Vega de León, Antonio, Chen, Beining, Gillet, Valerie J.

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.85 MB

english, 2018

34

P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure

Krivák, Radoslav, Hoksza, David

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.53 MB

english, 2018

35

Ambit-SMIRKS: a software module for reaction representation, reaction search and structure transformation

Kochev, Nikolay, Avramova, Svetlana, Jeliazkova, Nina

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 5.35 MB

english, 2018

36

HAMdb: a database of human autophagy modulators with specific pathway and disease information

Wang, Ning-Ning, Dong, Jie, Zhang, Lin, Ouyang, Defang, Cheng, Yan, Chen, Alex F., Lu, Ai-Ping, Cao, Dong-Sheng

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.17 MB

english, 2018

37

Putting hands to rest: efficient deep CNN-RNN architecture for chemical named entity recognition with no hand-crafted rules

Korvigo, Ilia, Holmatov, Maxim, Zaikovskii, Anatolii, Skoblov, Mikhail

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.24 MB

english, 2018

38

Multi-objective de novo drug design with conditional graph generative model

Li, Yibo, Zhang, Liangren, Liu, Zhenming

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 2.51 MB

english, 2018

39

Machine learning for the prediction of molecular dipole moments obtained by density functional theory

Pereira, Florbela, Aires-de-Sousa, João

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.30 MB

english, 2018

40

Probing the chemical–biological relationship space with the Drug Target Explorer

Allaway, Robert J., La Rosa, Salvatore, Guinney, Justin, Gosline, Sara J. C.

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 2.80 MB

english, 2018

41

RepTB: a gene ontology based drug repurposing approach for tuberculosis

Passi, Anurag, Rajput, Neeraj Kumar, Wild, David J., Bhardwaj, Anshu

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 2.12 MB

english, 2018

42

The influence of solid state information and descriptor selection on statistical models of temperature dependent aqueous solubility

Marchese Robinson, Richard L., Roberts, Kevin J., Martin, Elaine B.

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.82 MB

english, 2018

43

“MS-Ready” structures for non-targeted high-resolution mass spectrometry screening studies

McEachran, Andrew D., Mansouri, Kamel, Grulke, Chris, Schymanski, Emma L., Ruttkies, Christoph, Williams, Antony J.

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 3.72 MB

english, 2018

44

Novel applications of Machine Learning in cheminformatics

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 656 KB

english, 2018

45

Novel pharmacological maps of protein lysine methyltransferases: key for target deorphanization

Rabal, Obdulia, Castellar, Andrea, Oyarzabal, Julen

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 8.84 MB

english, 2018

46

Annotation and detection of drug effects in text for pharmacovigilance

Thompson, Paul, Daikou, Sophia, Ueno, Kenju, Batista-Navarro, Riza, Tsujii, Jun’ichi, Ananiadou, Sophia

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 9.38 MB

english, 2018

47

Exploring non-linear distance metrics in the structure–activity space: QSAR models for human estrogen receptor

Balabin, Ilya A., Judson, Richard S.

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.72 MB

english, 2018

48

SPICES: a particle-based molecular structure line notation and support library for mesoscopic simulation

van den Broek, Karina, Daniel, Mirco, Epple, Matthias, Kuhn, Hubert, Schaub, Jonas, Zielesny, Achim

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.87 MB

english, 2018

49

Life beyond the Tanimoto coefficient: similarity measures for interaction fingerprints

Rácz, Anita, Bajusz, Dávid, Héberger, Károly

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 3.11 MB

english, 2018

50

Chemotion-ELN part 2: adaption of an embedded Ketcher editor to advanced research applications

Kotov, Serhii, Tremouilhac, Pierre, Jung, Nicole, Bräse, Stefan

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.76 MB

english, 2018

51

Choquet integral-based fuzzy molecular characterizations: when global definitions are computed from the dependency among atom/bond contributions (LOVIs/LOEIs)

García-Jacas, César R., Cabrera-Leyva, Lisset, Marrero-Ponce, Yovani, Suárez-Lezcano, José, Cortés-Guzmán, Fernando, Pupo-Meriño, Mario, Vivas-Reyes, Ricardo

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 3.78 MB

english, 2018

52

An automated framework for NMR chemical shift calculations of small organic molecules

Yesiltepe, Yasemin, Nuñez, Jamie R., Colby, Sean M., Thomas, Dennis G., Borkum, Mark I., Reardon, Patrick N., Washton, Nancy M., Metz, Thomas O., Teeguarden, Justin G., Govind, Niranjan, Renslow, Ryan

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 2.54 MB

english, 2018

53

A new chemoinformatics approach with improved strategies for effective predictions of potential drugs

Hao, Ming, Bryant, Stephen H., Wang, Yanli

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.32 MB

english, 2018

54

Evaluating parameters for ligand-based modeling with random forest on sparse data sets

Kensert, Alexander, Alvarsson, Jonathan, Norinder, Ulf, Spjuth, Ola

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.92 MB

english, 2018

55

Cheminformatics-based enumeration and analysis of large libraries of macrolide scaffolds

Zin, Phyo Phyo Kyaw, Williams, Gavin, Fourches, Denis

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 5.40 MB

english, 2018

56

Improved understanding of aqueous solubility modeling through topological data analysis

Pirashvili, Mariam, Steinberg, Lee, Belchi Guillamon, Francisco, Niranjan, Mahesan, Frey, Jeremy G., Brodzki, Jacek

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 2.59 MB

english, 2018

57

Implicit-descriptor ligand-based virtual screening by means of collaborative filtering

Srinivas, Raghuram, Klimovich, Pavel V., Larson, Eric C.

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 2.50 MB

english, 2018

58

Chemlistem: chemical named entity recognition using recurrent neural networks

Corbett, Peter, Boyle, John

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 846 KB

english, 2018

59

A new semi-automated workflow for chemical data retrieval and quality checking for modeling applications

Gadaleta, Domenico, Lombardo, Anna, Toma, Cosimo, Benfenati, Emilio

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.75 MB

english, 2018

60

Chaos-embedded particle swarm optimization approach for protein-ligand docking and virtual screening

Tai, Hio Kuan, Jusoh, Siti Azma, Siu, Shirley W. I.

Journal:

Journal of Cheminformatics

Year:

2018

File:

PDF, 2.33 MB

2018

61

A neural network approach to chemical and gene/protein entity recognition in patents

Luo, Ling, Yang, Zhihao, Yang, Pei, Zhang, Yin, Wang, Lei, Wang, Jian, Lin, Hongfei

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.11 MB

english, 2018

62

SIA: a scalable interoperable annotation server for biomedical named entities

Kirschnick, Johannes, Thomas, Philippe, Roller, Roland, Hennig, Leonhard

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.06 MB

english, 2018

63

chemmodlab: a cheminformatics modeling laboratory R package for fitting and assessing machine learning models

Ash, Jeremy R., Hughes-Oliver, Jacqueline M.

Journal:

Journal of Cheminformatics

Year:

2018

File:

PDF, 1.44 MB

2018

64

JPlogP: an improved logP predictor trained using predicted data

Plante, Jeffrey, Werner, Stephane

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.49 MB

english, 2018

65

MER: a shell script and annotation server for minimal named entity recognition and linking

Couto, Francisco M., Lamurias, Andre

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 1.10 MB

english, 2018

66

Statistical-based database fingerprint: chemical space dependent representation of compound databases

Sánchez-Cruz, Norberto, Medina-Franco, José L.

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 2.46 MB

english, 2018

67

Configurable web-services for biomedical document annotation

Journal:

Journal of Cheminformatics

Year:

2018

Language:

english

File:

PDF, 2.28 MB

english, 2018

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