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ORCIDJournal of Cheminformatics, Volume 11
Volume 11, Number 1, December 2019
- Ian A. Watson, Ji-Bo Wang, Christos A. Nicolaou
:
A retrosynthetic analysis algorithm implementation. 1:1-1:12 - Yannick Djoumbou Feunang, Jarlei Fiamoncini, Alberto Gil-de-la-Fuente, Russell Greiner, Claudine Manach, David S. Wishart:
BioTransformer: a comprehensive computational tool for small molecule metabolism prediction and metabolite identification. 2:1-2:25 - Wahed Hemati, Alexander Mehler:
LSTMVoter: chemical named entity recognition using a conglomerate of sequence labeling tools. 3:1-3:7 - Nicolas Bosc, Francis Atkinson, Eloy Felix, Anna Gaulton, Anne Hersey, Andrew R. Leach:
Large scale comparison of QSAR and conformal prediction methods and their applications in drug discovery. 4:1-4:16 - Shuangjia Zheng, Xin Yan, Qiong Gu, Yuedong Yang, Yunfei Du, Yutong Lu, Jun Xu:
QBMG: quasi-biogenic molecule generator with deep recurrent neural network. 5:1-5:12 - Wenyi Wang, Xiliang Yan, Linlin Zhao, Daniel P. Russo, Shenqing Wang, Yin Liu, Alexander Sedykh, Xiaoli Zhao, Bing Yan, Hao Zhu:
Universal nanohydrophobicity predictions using virtual nanoparticle library. 6:1-6:5 - Lenz Furrer, Anna Jancso, Nicola Colic, Fabio Rinaldi:
OGER++: hybrid multi-type entity recognition. 7:1-7:10 - Peter W. Kenny:
The nature of ligand efficiency. 8:1-8:18 - Thierry Hanser, Fabian P. Steinmetz, Jeffrey Plante, Friedrich Rippmann, Mireille Krier:
Avoiding hERG-liability in drug design via synergetic combinations of different (Q)SAR methodologies and data sources: a case study in an industrial setting. 9:1-9:13 - Francois Berenger, Kam Y. J. Zhang, Yoshihiro Yamanishi:
Chemoinformatics and structural bioinformatics in OCaml. 10:1-10:13 - Kevin J. Theisen:
Programming languages in chemistry: a review of HTML5/JavaScript. 11:1-11:19 - Rajarshi Guha:
Implementing cheminformatics. 12:1-12:2 - Emma Ricart, Valérie Leclère, Areski Flissi, Markus Müller, Maude Pupin, Frédérique Lisacek:
rBAN: retro-biosynthetic analysis of nonribosomal peptides. 13:1-13:14 - Patrick J. Ropp, Jesse C. Kaminsky, Sara Yablonski, Jacob D. Durrant:
Dimorphite-DL: an open-source program for enumerating the ionization states of drug-like small molecules. 14:1-14:8 - Lindsey Burggraaff, Paul Oranje, Robin Gouka, Pieter van der Pijl, Marian Geldof, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen:
Identification of novel small molecule inhibitors for solute carrier SGLT1 using proteochemometric modeling. 15:1-15:10 - Ralf Weiskirchen, Sabine Weiskirchen, Philipp Kim, Robert Winkler:
Software solutions for evaluation and visualization of laser ablation inductively coupled plasma mass spectrometry imaging (LA-ICP-MSI) data: a short overview. 16:1-16:21 - Sera Park, Yeajee Kwon, Hyesoo Jung, Sukyung Jang, Haeseung Lee, Wan Kyu Kim:
CSgator: an integrated web platform for compound set analysis. 17:1-17:8 - Ivan D. Welsh, Jane R. Allison:
Automated simultaneous assignment of bond orders and formal charges. 18:1-18:12 - Sune Pletscher-Frankild, Lars Juhl Jensen:
Design, implementation, and operation of a rapid, robust named entity recognition web service. 19:1-19:6 - Josep Arús-Pous, Thomas Blaschke, Silas Ulander, Jean-Louis Reymond, Hongming Chen, Ola Engkvist:
Exploring the GDB-13 chemical space using deep generative models. 20:1-20:14 - Wahed Hemati, Alexander Mehler:
CRFVoter: gene and protein related object recognition using a conglomerate of CRF-based tools. 21:1-21:11 - Ying Shen, Kaiqi Yuan, Min Yang, Buzhou Tang, Yaliang Li, Nan Du, Kai Lei:
KMR: knowledge-oriented medicine representation learning for drug-drug interaction and similarity computation. 22:1-22:16 - Samantha Kanza, Nicholas Gibbins, Jeremy G. Frey:
Too many tags spoil the metadata: investigating the knowledge management of scientific research with semantic web technologies. 23:1-23:23 - Célien Jacquemard, Malgorzata N. Drwal, Jérémy Desaphy, Esther Kellenberger:
Binding mode information improves fragment docking. 24:1-24:15 - Daniela Kalafatovic, Goran Mausa, Toni Todorovski, Ernest Giralt:
Algorithm-supported, mass and sequence diversity-oriented random peptide library design. 25:1-25:15 - Willem Jespers, Mauricio Esguerra, Johan Åqvist, Hugo Gutiérrez-de-Terán:
QligFEP: an automated workflow for small molecule free energy calculations in Q. 26:1-26:16 - Kristijan Vukovic, Domenico Gadaleta, Emilio Benfenati:
Methodology of aiQSAR: a group-specific approach to QSAR modelling. 27:1-27:9 - Jian-Yu Shi, Kui-Tao Mao, Hui Yu, Siu-Ming Yiu:
Detecting drug communities and predicting comprehensive drug-drug interactions via balance regularized semi-nonnegative matrix factorization. 28:1-28:16 - Dominique Sydow, Andrea Morger, Maximilian Driller, Andrea Volkamer:
TeachOpenCADD: a teaching platform for computer-aided drug design using open source packages and data. 29:1-29:7 - Ankur Jai Sood, Coby Viner, Michael M. Hoffman:
DNAmod: the DNA modification database. 30:1-30:10 - Domenico Gadaleta, Anna Lombardo, Cosimo Toma, Emilio Benfenati:
Correction to: A new semi-automated workflow for chemical data retrieval and quality checking for modeling applications. 31:1 - Lucian Chan, Geoffrey R. Hutchison, Garrett M. Morris:
Bayesian optimization for conformer generation. 32:1-32:11 - Alex M. Clark, Leah McEwen, Peter Gedeck, Barry A. Bunin:
Capturing mixture composition: an open machine-readable format for representing mixed substances. 33:1-33:17 - Patrick J. Ropp, Jacob O. Spiegel, Jennifer L. Walker, Harrison Green, Guillermo A. Morales, Katherine A. Milliken, John J. Ringe, Jacob D. Durrant:
Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening. 34:1-34:13 - Xuhan Liu, Kai Ye, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen:
An exploration strategy improves the diversity of de novo ligands using deep reinforcement learning: a case for the adenosine A2A receptor. 35:1-35:16 - Chad H. G. Allen, Lewis H. Mervin, Samar Y. Mahmoud, Andreas Bender:
Leveraging heterogeneous data from GHS toxicity annotations, molecular and protein target descriptors and Tox21 assay readouts to predict and rationalise acute toxicity. 36:1-36:19 - Sebastian Fritsch, Stefan Neumann, Jonas Schaub, Christoph Steinbeck, Achim Zielesny:
ErtlFunctionalGroupsFinder: automated rule-based functional group detection with the Chemistry Development Kit (CDK). 37:1-37:8 - Angela Serra, Serli Önlü, Pietro Coretto, Dario Greco:
An integrated quantitative structure and mechanism of action-activity relationship model of human serum albumin binding. 38:1-38:10 - Inbal Tuvi-Arad, Gil Alon:
Improved algorithms for quantifying the near symmetry of proteins: complete side chains analysis. 39:1-39:11 - Eric W. Bell, Yang Zhang:
DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism. 40:1-40:9 - Isidro Cortes-Ciriano, Andreas Bender:
KekuleScope: prediction of cancer cell line sensitivity and compound potency using convolutional neural networks trained on compound images. 41:1-41:16 - Martín Pérez-Pérez, Gael Pérez Rodríguez, Aitor Blanco-Míguez, Florentino Fdez-Riverola, Alfonso Valencia, Martin Krallinger, Anália Lourenço:
Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm. 42:1-42:16 - Jeremy R. Ash, Mélaine A. Kuenemann, Daniel M. Rotroff, Alison A. Motsinger-Reif, Denis Fourches:
Cheminformatics approach to exploring and modeling trait-associated metabolite profiles. 43:1-43:15 - Egon L. Willighagen, Nina Jeliazkova, Rajarshi Guha:
Journal of Cheminformatics, ORCID, and GitHub. 44:1-44:2 - Miroslav Kratochvíl, Jirí Vondrásek, Jakub Galgonek:
Interoperable chemical structure search service. 45:1-45:7 - Munhwan Lee, Hyeyeon Kim, Hyunwhan Joe, Hong-Gee Kim:
Multi-channel PINN: investigating scalable and transferable neural networks for drug discovery. 46:1-46:16 - Lu Liang, Chunfeng Ma, Tengfei Du, Yufei Zhao, Xiaoyong Zhao, Mengmeng Liu, Zhonghua Wang, Jianping Lin:
Bioactivity-explorer: a web application for interactive visualization and exploration of bioactivity data. 47:1-47:6 - Lee Steinberg, John Russo, Jeremy G. Frey:
A new topological descriptor for water network structure. 48:1-48:11 - Naruki Yoshikawa, Geoffrey R. Hutchison:
Fast, efficient fragment-based coordinate generation for Open Babel. 49:1-49:9 - Eric Jonas, Stefan Kuhn:
Rapid prediction of NMR spectral properties with quantified uncertainty. 50:1-50:7 - Lee Steinberg, John Russo, Jeremy G. Frey:
Correction to: A new topological descriptor for water network structure. 51:1 - Pin Chen, Yaobin Ke, Yutong Lu, Yunfei Du, Jiahui Li, Hui Yan, Huiying Zhao, Yaoqi Zhou, Yuedong Yang:
DLIGAND2: an improved knowledge-based energy function for protein-ligand interactions using the distance-scaled, finite, ideal-gas reference state. 52:1-52:11 - Joel Wahl, Joël Freyss, Modest von Korff, Thomas Sander:
Accuracy evaluation and addition of improved dihedral parameters for the MMFF94s. 53:1-53:10 - Oliver Laufkötter, Noé Sturm, Jürgen Bajorath, Hongming Chen, Ola Engkvist:
Combining structural and bioactivity-based fingerprints improves prediction performance and scaffold hopping capability. 54:1-54:14 - Maria Sorokina, Christoph Steinbeck:
NaPLeS: a natural products likeness scorer - web application and database. 55:1-55:7 - Sunghwan Kim, Paul A. Thiessen, Tiejun Cheng, Jian Zhang, Asta Gindulyte, Evan Bolton:
PUG-View: programmatic access to chemical annotations integrated in PubChem. 56:1-56:11 - Simon Müller:
Flexible heuristic algorithm for automatic molecule fragmentation: application to the UNIFAC group contribution model. 57:1-57:12 - Domenico Gadaleta, Kristijan Vukovic, Cosimo Toma, Giovanna J. Lavado, Agnes L. Karmaus, Kamel Mansouri, Nicole C. Kleinstreuer, Emilio Benfenati, Alessandra Roncaglioni:
SAR and QSAR modeling of a large collection of LD50 rat acute oral toxicity data. 58:1-58:16 - Christoph Alexander Bauer, Gisbert Schneider, Andreas H. Göller:
Machine learning models for hydrogen bond donor and acceptor strengths using large and diverse training data generated by first-principles interaction free energies. 59:1-59:16 - Kamel Mansouri, Neal F. Cariello, Alexandru Korotcov, Valery Tkachenko, Christopher M. Grulke, Catherine S. Sprankle, David G. Allen, Warren M. Casey, Nicole C. Kleinstreuer, Antony J. Williams:
Open-source QSAR models for pKa prediction using multiple machine learning approaches. 60:1-60:20 - J. Jesús Naveja, B. Angélica Pilón-Jiménez, Jürgen Bajorath, José L. Medina-Franco:
A general approach for retrosynthetic molecular core analysis. 61:1-61:9 - Robert D. Clark:
A path to next-generation reproducibility in cheminformatics. 62:1-62:3 - Samina Kausar, André O. Falcão:
A visual approach for analysis and inference of molecular activity spaces. 63:1-63:17 - Nicolas Bosc, Francis Atkinson, Eloy Felix, Anna Gaulton, Anne Hersey, Andrew R. Leach:
Reply to "Missed opportunities in large scale comparison of QSAR and conformal prediction methods and their applications in drug discovery". 64:1-64:3 - Damjan Krstajic:
Missed opportunities in large scale comparison of QSAR and conformal prediction methods and their applications in drug discovery. 65:1-65:5 - David Ruano-Ordás, Lindsey Burggraaff, Rongfang Liu, Cas van der Horst, Laura H. Heitman, Michael T. M. Emmerich, José Ramón Méndez, Iryna Yevseyeva, Gerard J. P. van Westen:
A multiple classifier system identifies novel cannabinoid CB2 receptor ligands. 66:1-66:14 - Anna Lovrics, Veronika F. S. Pape, Dániel Szisz, Adrián Kalászi, Petra Heffeter, Csaba Magyar, Gergely Szakács:
Identifying new topoisomerase II poison scaffolds by combining publicly available toxicity data and 2D/3D-based virtual screening. 67:1-67:14 - Noureddin Sadawi, Iván Olier, Joaquin Vanschoren, Jan N. van Rijn, Jeremy Besnard, G. Richard J. Bickerton, Crina Grosan, Larisa N. Soldatova, Ross D. King:
Multi-task learning with a natural metric for quantitative structure activity relationship learning. 68:1-68:13 - Marta Glavatskikh, Jules Leguy, Gilles Hunault, Thomas Cauchy, Benoit Da Mota:
Dataset's chemical diversity limits the generalizability of machine learning predictions. 69:1-69:15 - Youngchun Kwon, Jiho Yoo, Youn-Suk Choi, Wonjoon Song, Dongseon Lee, Seokho Kang:
Efficient learning of non-autoregressive graph variational autoencoders for molecular graph generation. 70:1-70:10 - Josep Arús-Pous, Simon Johansson, Oleksii Prykhodko, Esben Jannik Bjerrum, Christian Tyrchan, Jean-Louis Reymond, Hongming Chen, Ola Engkvist:
Randomized SMILES strings improve the quality of molecular generative models. 71:1-71:13 - Robin Haunschild, Andreas Barth, Bernie French:
A comprehensive analysis of the history of DFT based on the bibliometric method RPYS. 72:1-72:15 - Fan Wang, Feng-Xu Wu, Cheng-Zhang Li, Chen-Yang Jia, Sun-Wen Su, Ge-Fei Hao, Guangfu Yang:
ACID: a free tool for drug repurposing using consensus inverse docking strategy. 73:1-73:11 - Oleksii Prykhodko, Simon Johansson, Panagiotis-Christos Kotsias, Josep Arús-Pous, Esben Jannik Bjerrum, Ola Engkvist, Hongming Chen:
A de novo molecular generation method using latent vector based generative adversarial network. 74 - Julien Wist:
HastaLaVista, a web-based user interface for NMR-based untargeted metabolic profiling analysis in biomedical sciences: towards a new publication standard. 75 - Andrew Dalke:
The chemfp project. 76 - An Nguyen, Yu-Chieh Huang, Pierre Tremouilhac, Nicole Jung, Stefan Bräse:
ChemScanner: extraction and re-use(ability) of chemical information from common scientific documents containing ChemDraw files. 77 - Pei-Hua Wang, Yufeng Jane Tseng:
IntelliPatent: a web-based intelligent system for fast chemical patent claim drafting. 78 - Xujun Liang, Pengfei Zhang, Jun Li, Ying Fu, Lingzhi Qu, Yongheng Chen, Zhuchu Chen:
Learning important features from multi-view data to predict drug side effects. 79 - Stefan Höck, Rainer Riedl:
CyBy2: a strongly typed, purely functional framework for chemical data management. 80
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