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Volume 11; Issue 1
Main
Journal of Cheminformatics
Volume 11; Issue 1
Journal of Cheminformatics
Volume 11; Issue 1
1
Dimorphite-DL: an open-source program for enumerating the ionization states of drug-like small molecules
Ropp, Patrick J.
,
Kaminsky, Jesse C.
,
Yablonski, Sara
,
Durrant, Jacob D.
Journal:
Journal of Cheminformatics
Year:
2019
File:
PDF, 1.06 MB
Your tags:
2019
2
Programming languages in chemistry: a review of HTML5/JavaScript
Theisen, Kevin J.
Journal:
Journal of Cheminformatics
Year:
2019
File:
PDF, 1.03 MB
Your tags:
2019
3
QBMG: quasi-biogenic molecule generator with deep recurrent neural network
Zheng, Shuangjia
,
Yan, Xin
,
Gu, Qiong
,
Yang, Yuedong
,
Du, Yunfei
,
Lu, Yutong
,
Xu, Jun
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 1.70 MB
Your tags:
english, 2019
4
OGER++: hybrid multi-type entity recognition
Furrer, Lenz
,
Jancso, Anna
,
Colic, Nicola
,
Rinaldi, Fabio
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 1.60 MB
Your tags:
english, 2019
5
Chemoinformatics and structural bioinformatics in OCaml
Berenger, Francois
,
Zhang, Kam Y. J.
,
Yamanishi, Yoshihiro
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 1.63 MB
Your tags:
english, 2019
6
Binding mode information improves fragment docking
Jacquemard, Célien
,
Drwal, Malgorzata N.
,
Desaphy, Jérémy
,
Kellenberger, Esther
Journal:
Journal of Cheminformatics
Year:
2019
File:
PDF, 5.62 MB
Your tags:
2019
7
Algorithm-supported, mass and sequence diversity-oriented random peptide library design
Kalafatovic, Daniela
,
Mauša, Goran
,
Todorovski, Toni
,
Giralt, Ernest
Journal:
Journal of Cheminformatics
Year:
2019
File:
PDF, 5.10 MB
Your tags:
2019
8
Binding mode information improves fragment docking
Jacquemard, Célien
,
Drwal, Malgorzata N.
,
Desaphy, Jérémy
,
Kellenberger, Esther
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 5.62 MB
Your tags:
english, 2019
9
QligFEP: an automated workflow for small molecule free energy calculations in Q
Jespers, Willem
,
Esguerra, Mauricio
,
Åqvist, Johan
,
Gutiérrez-de-Terán, Hugo
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 2.30 MB
Your tags:
english, 2019
10
DNAmod: the DNA modification database
Sood, Ankur Jai
,
Viner, Coby
,
Hoffman, Michael M.
Journal:
Journal of Cheminformatics
Year:
2019
File:
PDF, 2.50 MB
Your tags:
2019
11
Exploring the GDB-13 chemical space using deep generative models
Arús-Pous, Josep
,
Blaschke, Thomas
,
Ulander, Silas
,
Reymond, Jean-Louis
,
Chen, Hongming
,
Engkvist, Ola
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 3.04 MB
Your tags:
english, 2019
12
CRFVoter: gene and protein related object recognition using a conglomerate of CRF-based tools
Hemati, Wahed
,
Mehler, Alexander
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 1.15 MB
Your tags:
english, 2019
13
Correction to: 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:
2019
Language:
english
File:
PDF, 608 KB
Your tags:
english, 2019
14
An exploration strategy improves the diversity of de novo ligands using deep reinforcement learning: a case for the adenosine A2A receptor
Liu, Xuhan
,
Ye, Kai
,
van Vlijmen, Herman W. T.
,
IJzerman, Adriaan P.
,
van Westen, Gerard J. P.
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 7.53 MB
Your tags:
english, 2019
15
Capturing mixture composition: an open machine-readable format for representing mixed substances
Clark, Alex M.
,
McEwen, Leah R.
,
Gedeck, Peter
,
Bunin, Barry A.
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 2.92 MB
Your tags:
english, 2019
16
Leveraging heterogeneous data from GHS toxicity annotations, molecular and protein target descriptors and Tox21 assay readouts to predict and rationalise acute toxicity
Allen, Chad H. G.
,
Mervin, Lewis H.
,
Mahmoud, Samar Y.
,
Bender, Andreas
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 3.42 MB
Your tags:
english, 2019
17
ErtlFunctionalGroupsFinder: automated rule-based functional group detection with the Chemistry Development Kit (CDK)
Fritsch, Sebastian
,
Neumann, Stefan
,
Schaub, Jonas
,
Steinbeck, Christoph
,
Zielesny, Achim
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 1.72 MB
Your tags:
english, 2019
18
An integrated quantitative structure and mechanism of action-activity relationship model of human serum albumin binding
Serra, Angela
,
Önlü, Serli
,
Coretto, Pietro
,
Greco, Dario
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 1.33 MB
Your tags:
english, 2019
19
Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening
Ropp, Patrick J.
,
Spiegel, Jacob O.
,
Walker, Jennifer L.
,
Green, Harrison
,
Morales, Guillermo A.
,
Milliken, Katherine A.
,
Ringe, John J.
,
Durrant, Jacob D.
Journal:
Journal of Cheminformatics
Year:
2019
File:
PDF, 2.25 MB
Your tags:
2019
20
An exploration strategy improves the diversity of de novo ligands using deep reinforcement learning: a case for the adenosine A2A receptor
Liu, Xuhan
,
Ye, Kai
,
van Vlijmen, Herman W. T.
,
IJzerman, Adriaan P.
,
van Westen, Gerard J. P.
Journal:
Journal of Cheminformatics
Year:
2019
File:
PDF, 7.53 MB
Your tags:
2019
21
Improved algorithms for quantifying the near symmetry of proteins: complete side chains analysis
Tuvi-Arad, Inbal
,
Alon, Gil
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 1.81 MB
Your tags:
english, 2019
22
DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism
Bell, Eric W.
,
Zhang, Yang
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 3.08 MB
Your tags:
english, 2019
23
Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm
Pérez-Pérez, Martin
,
Pérez-Rodríguez, Gael
,
Blanco-Míguez, Aitor
,
Fdez-Riverola, Florentino
,
Valencia, Alfonso
,
Krallinger, Martin
,
Lourenço, Anália
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 2.17 MB
Your tags:
english, 2019
24
An integrated quantitative structure and mechanism of action-activity relationship model of human serum albumin binding
Serra, Angela
,
Önlü, Serli
,
Coretto, Pietro
,
Greco, Dario
Journal:
Journal of Cheminformatics
Year:
2019
File:
PDF, 1.33 MB
Your tags:
2019
25
Bioactivity-explorer: a web application for interactive visualization and exploration of bioactivity data
Liang, Lu
,
Ma, Chunfeng
,
Du, Tengfei
,
Zhao, Yufei
,
Zhao, Xiaoyong
,
Liu, Mengmeng
,
Wang, Zhonghua
,
Lin, Jianping
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 1.22 MB
Your tags:
english, 2019
26
Journal of Cheminformatics, ORCID, and GitHub
Willighagen, Egon
,
Jeliazkova, Nina
,
Guha, Rajarshi
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 886 KB
Your tags:
english, 2019
27
Interoperable chemical structure search service
Kratochvíl, Miroslav
,
Vondrášek, Jiří
,
Galgonek, Jakub
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 1.31 MB
Your tags:
english, 2019
28
Multi-channel PINN: investigating scalable and transferable neural networks for drug discovery
Lee, Munhwan
,
Kim, Hyeyeon
,
Joe, Hyunwhan
,
Kim, Hong-Gee
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 1.80 MB
Your tags:
english, 2019
29
A new topological descriptor for water network structure
Steinberg, Lee
,
Russo, John
,
Frey, Jeremy
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 2.34 MB
Your tags:
english, 2019
30
A new topological descriptor for water network structure
Steinberg, Lee
,
Russo, John
,
Frey, Jeremy
Journal:
Journal of Cheminformatics
Year:
2019
File:
PDF, 2.34 MB
Your tags:
2019
31
Accuracy evaluation and addition of improved dihedral parameters for the MMFF94s
Wahl, Joel
,
Freyss, Joel
,
von Korff, Modest
,
Sander, Thomas
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 1.45 MB
Your tags:
english, 2019
32
Combining structural and bioactivity-based fingerprints improves prediction performance and scaffold hopping capability
Laufkötter, Oliver
,
Sturm, Noé
,
Bajorath, Jürgen
,
Chen, Hongming
,
Engkvist, Ola
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 2.06 MB
Your tags:
english, 2019
33
DLIGAND2: an improved knowledge-based energy function for protein–ligand interactions using the distance-scaled, finite, ideal-gas reference state
Chen, Pin
,
Ke, Yaobin
,
Lu, Yutong
,
Du, Yunfei
,
Li, Jiahui
,
Yan, Hui
,
Zhao, Huiying
,
Zhou, Yaoqi
,
Yang, Yuedong
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 1.42 MB
Your tags:
english, 2019
34
Fast, efficient fragment-based coordinate generation for Open Babel
Yoshikawa, Naruki
,
Hutchison, Geoffrey R.
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 1.11 MB
Your tags:
english, 2019
35
Correction to: A new topological descriptor for water network structure
Steinberg, Lee
,
Russo, John
,
Frey, Jeremy
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 674 KB
Your tags:
english, 2019
36
NaPLeS: a natural products likeness scorer—web application and database
Sorokina, Maria
,
Steinbeck, Christoph
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 1.52 MB
Your tags:
english, 2019
37
Flexible heuristic algorithm for automatic molecule fragmentation: application to the UNIFAC group contribution model
Müller, Simon
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 975 KB
Your tags:
english, 2019
38
Open-source QSAR models for pKa prediction using multiple machine learning approaches
Mansouri, Kamel
,
Cariello, Neal F.
,
Korotcov, Alexandru
,
Tkachenko, Valery
,
Grulke, Chris M.
,
Sprankle, Catherine S.
,
Allen, David
,
Casey, Warren M.
,
Kleinstreuer, Nicole C.
,
Williams, Antony J.
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 4.86 MB
Your tags:
english, 2019
39
Open-source QSAR models for pKa prediction using multiple machine learning approaches
Mansouri, Kamel
,
Cariello, Neal F.
,
Korotcov, Alexandru
,
Tkachenko, Valery
,
Grulke, Chris M.
,
Sprankle, Catherine S.
,
Allen, David
,
Casey, Warren M.
,
Kleinstreuer, Nicole C.
,
Williams, Antony J.
Journal:
Journal of Cheminformatics
Year:
2019
File:
PDF, 4.86 MB
Your tags:
2019
40
Machine learning models for hydrogen bond donor and acceptor strengths using large and diverse training data generated by first-principles interaction free energies
Bauer, Christoph A.
,
Schneider, Gisbert
,
Göller, Andreas H.
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 2.50 MB
Your tags:
english, 2019
41
Machine learning models for hydrogen bond donor and acceptor strengths using large and diverse training data generated by first-principles interaction free energies
Bauer, Christoph A.
,
Schneider, Gisbert
,
Göller, Andreas H.
Journal:
Journal of Cheminformatics
Year:
2019
File:
PDF, 2.50 MB
Your tags:
2019
42
A retrosynthetic analysis algorithm implementation
Watson, Ian A.
,
Wang, Jibo
,
Nicolaou, Christos A.
Journal:
Journal of Cheminformatics
Year:
2019
File:
PDF, 1.73 MB
Your tags:
2019
43
Randomized SMILES strings improve the quality of molecular generative models
Arús-Pous, Josep
,
Johansson, Simon Viet
,
Prykhodko, Oleksii
,
Bjerrum, Esben Jannik
,
Tyrchan, Christian
,
Reymond, Jean-Louis
,
Chen, Hongming
,
Engkvist, Ola
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 2.06 MB
Your tags:
english, 2019
44
Dataset’s chemical diversity limits the generalizability of machine learning predictions
Glavatskikh, Marta
,
Leguy, Jules
,
Hunault, Gilles
,
Cauchy, Thomas
,
Da Mota, Benoit
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 2.46 MB
Your tags:
english, 2019
45
ChemScanner: extraction and re-use(ability) of chemical information from common scientific documents containing ChemDraw files
Nguyen, An
,
Huang, Yu-Chieh
,
Tremouilhac, Pierre
,
Jung, Nicole
,
Bräse, Stefan
Journal:
Journal of Cheminformatics
Year:
2019
Language:
english
File:
PDF, 1.67 MB
Your tags:
english, 2019
46
ACID: a free tool for drug repurposing using consensus inverse docking strategy
Wang, Fan
,
Wu, Feng-Xu
,
Li, Cheng-Zhang
,
Jia, Chen-Yang
,
Su, Sun-Wen
,
Hao, Ge-Fei
,
Yang, Guang-Fu
Journal:
Journal of Cheminformatics
Year:
2019
File:
PDF, 1.47 MB
Your tags:
2019
47
Randomized SMILES strings improve the quality of molecular generative models
Arús-Pous, Josep
,
Johansson, Simon Viet
,
Prykhodko, Oleksii
,
Bjerrum, Esben Jannik
,
Tyrchan, Christian
,
Reymond, Jean-Louis
,
Chen, Hongming
,
Engkvist, Ola
Journal:
Journal of Cheminformatics
Year:
2019
File:
PDF, 2.06 MB
Your tags:
2019
48
Efficient learning of non-autoregressive graph variational autoencoders for molecular graph generation
Kwon, Youngchun
,
Yoo, Jiho
,
Choi, Youn-Suk
,
Son, Won-Joon
,
Lee, Dongseon
,
Kang, Seokho
Journal:
Journal of Cheminformatics
Year:
2019
File:
PDF, 1.83 MB
Your tags:
2019
49
Multi-task learning with a natural metric for quantitative structure activity relationship learning
Sadawi, Noureddin
,
Olier, Ivan
,
Vanschoren, Joaquin
,
van Rijn, Jan N.
,
Besnard, Jeremy
,
Bickerton, Richard
,
Grosan, Crina
,
Soldatova, Larisa
,
King, Ross D.
Journal:
Journal of Cheminformatics
Year:
2019
File:
PDF, 1.38 MB
Your tags:
2019
50
Dataset’s chemical diversity limits the generalizability of machine learning predictions
Glavatskikh, Marta
,
Leguy, Jules
,
Hunault, Gilles
,
Cauchy, Thomas
,
Da Mota, Benoit
Journal:
Journal of Cheminformatics
Year:
2019
File:
PDF, 2.46 MB
Your tags:
2019
51
ChemScanner: extraction and re-use(ability) of chemical information from common scientific documents containing ChemDraw files
Nguyen, An
,
Huang, Yu-Chieh
,
Tremouilhac, Pierre
,
Jung, Nicole
,
Bräse, Stefan
Journal:
Journal of Cheminformatics
Year:
2019
File:
PDF, 1.67 MB
Your tags:
2019
52
A path to next-generation reproducibility in cheminformatics
Clark, Robert D.
Journal:
Journal of Cheminformatics
Year:
2019
File:
PDF, 855 KB
Your tags:
2019
53
A de novo molecular generation method using latent vector based generative adversarial network
Prykhodko, Oleksii
,
Johansson, Simon Viet
,
Kotsias, Panagiotis-Christos
,
Arús-Pous, Josep
,
Bjerrum, Esben Jannik
,
Engkvist, Ola
,
Chen, Hongming
Journal:
Journal of Cheminformatics
Year:
2019
File:
PDF, 3.43 MB
Your tags:
2019
54
Missed opportunities in large scale comparison of QSAR and conformal prediction methods and their applications in drug discovery
Krstajic, Damjan
Journal:
Journal of Cheminformatics
Year:
2019
File:
PDF, 816 KB
Your tags:
2019
55
Learning important features from multi-view data to predict drug side effects
Liang, Xujun
,
Zhang, Pengfei
,
Li, Jun
,
Fu, Ying
,
Qu, Lingzhi
,
Chen, Yongheng
,
Chen, Zhuchu
Journal:
Journal of Cheminformatics
Year:
2019
File:
PDF, 2.03 MB
Your tags:
2019
56
The chemfp project
Dalke, Andrew
Journal:
Journal of Cheminformatics
Year:
2019
File:
PDF, 1.10 MB
Your tags:
2019
57
HastaLaVista, a web-based user interface for NMR-based untargeted metabolic profiling analysis in biomedical sciences: towards a new publication standard
Wist, Julien
Journal:
Journal of Cheminformatics
Year:
2019
File:
PDF, 2.15 MB
Your tags:
2019
58
IntelliPatent: a web-based intelligent system for fast chemical patent claim drafting
Wang, Pei-Hua
,
Tseng, Yufeng Jane
Journal:
Journal of Cheminformatics
Year:
2019
File:
PDF, 2.12 MB
Your tags:
2019
59
CyBy2: a strongly typed, purely functional framework for chemical data management
Höck, Stefan
,
Riedl, Rainer
Journal:
Journal of Cheminformatics
Year:
2019
File:
PDF, 2.08 MB
Your tags:
2019
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