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ORCIDJournal of Cheminformatics, Volume 12
Volume 12, Number 1, December 2020
- Michael Withnall
, Edvard Lindelöf, Ola Engkvist, Hongming Chen:
Building attention and edge message passing neural networks for bioactivity and physical-chemical property prediction. 1 - Lukasz Maziarka, Agnieszka Pocha, Jan Kaczmarczyk, Krzysztof Rataj, Tomasz Danel, Michal Warchol:
Mol-CycleGAN: a generative model for molecular optimization. 2 - Adrian Voicu, Narcis Duteanu, Mirela Voicu, Daliborca Vlad, Victor Dumitrascu:
The rcdk and cluster R packages applied to drug candidate selection. 3 - Rajarshi Guha, Egon L. Willighagen:
Learning cheminformatics. 4 - Gergely Zahoránszky-Köhalmi, Timothy Sheils, Tudor I. Oprea:
SmartGraph: a network pharmacology investigation platform. 5 - Myungwon Seo, Hyun Kil Shin, Yoochan Myung, Sungbo Hwang, Kyoung Tai No:
Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development. 6 - Pin Chen, Yu Wang, Hui Yan, Sen Gao, Zexin Xu, Yangzhong Li, Qing Mo, Junkang Huang, Jun Tao, GeChuanqi Pan, Jiahui Li, Yunfei Du:
3DStructGen: an interactive web-based 3D structure generation for non-periodic molecule and crystal. 7 - Peter Ertl:
Craig plot 2.0: an interactive navigation in the substituent bioisosteric space. 8 - Nalini Schaduangrat, Samuel Lampa, Saw Simeon, Matthew Paul Gleeson, Ola Spjuth, Chanin Nantasenamat:
Towards reproducible computational drug discovery. 9 - Dmitrii N. Rassokhin:
The C++ programming language in cheminformatics and computational chemistry. 10 - Benoit Playe, Véronique Stoven:
Evaluation of deep and shallow learning methods in chemogenomics for the prediction of drugs specificity. 11 - Daniel Probst, Jean-Louis Reymond:
Visualization of very large high-dimensional data sets as minimum spanning trees. 12 - Miroslav Kratochvíl, Jirí Vondrásek, Jakub Galgonek:
Correction to: Interoperable chemical structure search service. 13 - Jacob Yasonik:
Multiobjective de novo drug design with recurrent neural networks and nondominated sorting. 14 - Bowen Tang, Skyler T. Kramer, Meijuan Fang, Yingkun Qiu, Zhen Wu, Dong Xu:
A self-attention based message passing neural network for predicting molecular lipophilicity and aqueous solubility. 15 - Dejun Jiang, Tailong Lei, Zhe Wang, Chao Shen, Dong-Sheng Cao, Tingjun Hou:
ADMET evaluation in drug discovery. 20. Prediction of breast cancer resistance protein inhibition through machine learning. 16 - Pavel Karpov, Guillaume Godin, Igor V. Tetko:
Transformer-CNN: Swiss knife for QSAR modeling and interpretation. 17 - Jennifer Hemmerich, Ece Asilar, Gerhard F. Ecker:
COVER: conformational oversampling as data augmentation for molecules. 18 - Chia-Hsiu Chen, Kenichi Tanaka, Masaaki Kotera, Kimito Funatsu:
Comparison and improvement of the predictability and interpretability with ensemble learning models in QSPR applications. 19 - Maria Sorokina, Christoph Steinbeck:
Review on natural products databases: where to find data in 2020. 20 - Pranav Shah, Vishal B. Siramshetty, Alexey V. Zakharov, Noel Southall, Xin Xu, Dac-Trung Nguyen:
Predicting liver cytosol stability of small molecules. 21 - Ruud van Deursen, Peter Ertl, Igor V. Tetko, Guillaume Godin:
GEN: highly efficient SMILES explorer using autodidactic generative examination networks. 22 - Phyo Phyo Kyaw Zin, Gavin Williams, Denis Fourches:
SIME: synthetic insight-based macrolide enumerator to generate the V1B library of 1 billion macrolides. 23 - Andrea Morger, Miriam Mathea, Janosch Achenbach, Antje Wolf, Roland Buesen, Klaus-Jürgen Schleifer, Robert Landsiedel, Andrea Volkamer:
KnowTox: pipeline and case study for confident prediction of potential toxic effects of compounds in early phases of development. 24 - Jacob O. Spiegel, Jacob D. Durrant:
AutoGrow4: an open-source genetic algorithm for de novo drug design and lead optimization. 25 - Noé Sturm, Andreas Mayr, Thanh Le Van, Vladimir I. Chupakhin, Hugo Ceulemans, Jörg K. Wegner, José Felipe Golib Dzib, Nina Jeliazkova, Yves Vandriessche, Stanislav Böhm, Vojtech Cima, Jan Martinovic, Nigel Greene, Tom Vander Aa, Thomas J. Ashby, Sepp Hochreiter, Ola Engkvist, Günter Klambauer, Hongming Chen:
Industry-scale application and evaluation of deep learning for drug target prediction. 26 - Xinhao Li, Denis Fourches:
Inductive transfer learning for molecular activity prediction: Next-Gen QSAR Models with MolPMoFiT. 27 - Pavel G. Polishchuk:
CReM: chemically reasonable mutations framework for structure generation. 28 - Karina van den Broek, Mirco Daniel, Matthias Epple, Jan-Mathis Hein, Hubert Kuhn, Stefan Neumann, Andreas Truszkowski, Achim Zielesny:
MFsim - an open Java all-in-one rich-client simulation environment for mesoscopic simulation. 29 - Esteban Lanzarotti, Lucas A. Defelipe, Marcelo A. Marti, Adrian Gustavo Turjanski:
Aromatic clusters in protein-protein and protein-drug complexes. 30 - Xiangyue Liu, Stefan Truppe, Gerard Meijer, Jesús Pérez-Ríos:
The diatomic molecular spectroscopy database. 31 - Ryosuke Kojima, Shoichi Ishida, Masateru Ohta, Hiroaki Iwata, Teruki Honma, Yasushi Okuno:
kGCN: a graph-based deep learning framework for chemical structures. 32 - Lindsey Burggraaff, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen:
Quantitative prediction of selectivity between the A1 and A2A adenosine receptors. 33 - Javed Iqbal, Martin Vogt, Jürgen Bajorath:
Activity landscape image analysis using convolutional neural networks. 34 - Milan Vorsilák, Michal Kolár, Ivan Cmelo, Daniel Svozil:
SYBA: Bayesian estimation of synthetic accessibility of organic compounds. 35 - Raquel Rodríguez-Pérez, Filip Miljkovic, Jürgen Bajorath:
Assessing the information content of structural and protein-ligand interaction representations for the classification of kinase inhibitor binding modes via machine learning and active learning. 36 - Wenyi Zhang, Eric W. Bell, Minghao Yin, Yang Zhang:
EDock: blind protein-ligand docking by replica-exchange monte carlo simulation. 37 - Josep Arús-Pous, Atanas Patronov, Esben Jannik Bjerrum, Christian Tyrchan, Jean-Louis Reymond, Hongming Chen, Ola Engkvist:
SMILES-based deep generative scaffold decorator for de-novo drug design. 38 - Ctibor Skuta, Isidro Cortes-Ciriano, Wim Dehaen, Pavel Kríz, Gerard J. P. van Westen, Igor V. Tetko, Andreas Bender, Daniel Svozil:
QSAR-derived affinity fingerprints (part 1): fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping. 39 - Simon Bray, Xavier Lucas, Anup Kumar, Björn A. Grüning:
The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform. 40 - Isidro Cortés-Ciriano, Ctibor Skuta, Andreas Bender, Daniel Svozil:
QSAR-derived affinity fingerprints (part 2): modeling performance for potency prediction. 41 - Xuanyi Li, Yinqiu Xu, Hequan Yao, Kejiang Lin:
Chemical space exploration based on recurrent neural networks: applications in discovering kinase inhibitors. 42 - Alice Capecchi, Daniel Probst, Jean-Louis Reymond:
One molecular fingerprint to rule them all: drugs, biomolecules, and the metabolome. 43 - Maha A. Thafar, Rawan S. Olayan, Haitham Ashoor, Somayah Albaradei, Vladimir B. Bajic, Xin Gao, Takashi Gojobori, Magbubah Essack:
DTiGEMS+: drug-target interaction prediction using graph embedding, graph mining, and similarity-based techniques. 44 - Gerard Baquer, Lluc Sementé, María García-Altares, Young Jin Lee, Pierre Chaurand, Xavier Correig, Pere Ràfols:
rMSIcleanup: an open-source tool for matrix-related peak annotation in mass spectrometry imaging and its application to silver-assisted laser desorption/ionization. 45 - Tamer N. Jarada, Jon G. Rokne, Reda Alhajj:
A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions. 46 - Egon L. Willighagen:
Adoption of the Citation Typing Ontology by the Journal of Cheminformatics. 47 - Dmytro G. Krotko:
Atomic ring invariant and Modified CANON extended connectivity algorithm for symmetry perception in molecular graphs and rigorous canonicalization of SMILES. 48 - Rocco Meli, Philip C. Biggin:
spyrmsd: symmetry-corrected RMSD calculations in Python. 49 - Tingjun Xu, Weiming Chen, Junhong Zhou, Jingfang Dai, Yingyong Li, Yingli Zhao:
Neural machine translation of chemical nomenclature between English and Chinese. 50 - A. Patrícia Bento, Anne Hersey, Eloy Felix, Gregory A. Landrum, Anna Gaulton, Francis Atkinson, Louisa J. Bellis, Marleen De Veij, Andrew R. Leach:
An open source chemical structure curation pipeline using RDKit. 51 - Ryosuke Shibukawa, Shoichi Ishida, Kazuki Yoshizoe, Kunihiro Wasa, Kiyosei Takasu, Yasushi Okuno, Kei Terayama, Koji Tsuda:
CompRet: a comprehensive recommendation framework for chemical synthesis planning with algorithmic enumeration. 52 - Yash Khemchandani, Stephen O'Hagan, Soumitra Samanta, Neil Swainston, Timothy J. Roberts, Danushka Bollegala, Douglas B. Kell:
DeepGraphMolGen, a multi-objective, computational strategy for generating molecules with desirable properties: a graph convolution and reinforcement learning approach. 53 - Simon Bray, Tharindu Senapathi, Christopher B. Barnett, Björn A. Grüning:
Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial. 54 - Jules Leguy, Thomas Cauchy, Marta Glavatskikh, Béatrice Duval, Benoit Da Mota:
EvoMol: a flexible and interpretable evolutionary algorithm for unbiased de novo molecular generation. 55 - Laurianne David, Amol Thakkar, Rocío Mercado, Ola Engkvist:
Molecular representations in AI-driven drug discovery: a review and practical guide. 56 - Pedro Ruas, Andre Lamurias, Francisco M. Couto:
Linking chemical and disease entities to ontologies by integrating PageRank with extracted relations from literature. 57 - Youngchun Kwon, Dongseon Lee, Youn-Suk Choi, Kyoham Shin, Seokho Kang:
Compressed graph representation for scalable molecular graph generation. 58 - Andrew Dalke:
Correction to: The chemfp project. 59 - Kohulan Rajan, Henning Otto Brinkhaus, Achim Zielesny, Christoph Steinbeck:
A review of optical chemical structure recognition tools. 60 - Aurelio Antelo-Collado, Ramón Carrasco-Velar, Nicolás García-Pedrajas, Gonzalo Cerruela García:
Maximum common property: a new approach for molecular similarity. 61 - Laeeq Ahmed, Hiba Alogheli, Staffan Arvidsson McShane, Jonathan Alvarsson, Arvid Berg, Anders Larsson, Wesley Schaal, Erwin Laure, Ola Spjuth:
Predicting target profiles with confidence as a service using docking scores. 62 - Shunyang Wang, Tobias Kind, Dean J. Tantillo, Oliver Fiehn:
Predicting in silico electron ionization mass spectra using quantum chemistry. 63 - Fernanda I. Saldívar-González, C. Sebastian Huerta-García, José L. Medina-Franco:
Chemoinformatics-based enumeration of chemical libraries: a tutorial. 64 - Kohulan Rajan, Achim Zielesny, Christoph Steinbeck:
DECIMER: towards deep learning for chemical image recognition. 65 - Gabriel Idakwo, Sundar Thangapandian, Joseph Luttrell IV, Yan Li, Nan Wang, Zhaoxian Zhou, Huixiao Hong, Bei Yang, Chaoyang Zhang, Ping Gong:
Structure-activity relationship-based chemical classification of highly imbalanced Tox21 datasets. 66 - Jonas Schaub, Achim Zielesny, Christoph Steinbeck, Maria Sorokina:
Too sweet: cheminformatics for deglycosylation in natural products. 67 - Emily J. Ha, Cara T. Lwin, Jacob D. Durrant:
LigGrep: a tool for filtering docked poses to improve virtual-screening hit rates. 69 - Samuel Genheden, Amol Thakkar, Veronika Chadimová, Jean-Louis Reymond, Ola Engkvist, Esben Jannik Bjerrum:
AiZynthFinder: a fast, robust and flexible open-source software for retrosynthetic planning. 70 - Alzbeta Türková, Barbara Zdrazil:
A ligand-based computational drug repurposing pipeline using KNIME and Programmatic Data Access: case studies for rare diseases and COVID-19. 71 - Victorien Delannée, Marc C. Nicklaus:
ReactionCode: format for reaction searching, analysis, classification, transform, and encoding/decoding. 72 - Jördis-Ann Schüler, Steffen Rechner, Matthias Müller-Hannemann:
MET: a Java package for fast molecule equivalence testing. 73 - Igor V. Tetko, Ola Engkvist:
From Big Data to Artificial Intelligence: chemoinformatics meets new challenges. 74
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