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Journal of Cheminformatics, Volume 12
Volume 12, Number 1, December 2020
- Michael Withnall
, Edvard Lindelöf, Ola Engkvist
Building attention and edge message passing neural networks for bioactivity and physical-chemical property prediction. 1 - Lukasz Maziarka
Mol-CycleGAN: a generative model for molecular optimization. 2 - Adrian Voicu, Narcis Duteanu
The rcdk and cluster R packages applied to drug candidate selection. 3 - Rajarshi Guha
Learning cheminformatics. 4 - Gergely Zahoránszky-Köhalmi
SmartGraph: a network pharmacology investigation platform. 5 - Myungwon Seo
Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development. 6 - Pin Chen
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
Towards reproducible computational drug discovery. 9 - Dmitrii N. Rassokhin
The C++ programming language in cheminformatics and computational chemistry. 10 - Benoit Playe
Evaluation of deep and shallow learning methods in chemogenomics for the prediction of drugs specificity. 11 - Daniel Probst
Visualization of very large high-dimensional data sets as minimum spanning trees. 12 - Miroslav Kratochvíl
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
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
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
Review on natural products databases: where to find data in 2020. 20 - Pranav Shah
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
SIME: synthetic insight-based macrolide enumerator to generate the V1B library of 1 billion macrolides. 23 - Andrea Morger
KnowTox: pipeline and case study for confident prediction of potential toxic effects of compounds in early phases of development. 24 - Jacob O. Spiegel
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
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
MFsim - an open Java all-in-one rich-client simulation environment for mesoscopic simulation. 29 - Esteban Lanzarotti, Lucas A. Defelipe
Aromatic clusters in protein-protein and protein-drug complexes. 30 - Xiangyue Liu
The diatomic molecular spectroscopy database. 31 - Ryosuke Kojima
kGCN: a graph-based deep learning framework for chemical structures. 32 - Lindsey Burggraaff
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
SYBA: Bayesian estimation of synthetic accessibility of organic compounds. 35 - Raquel Rodríguez-Pérez
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
EDock: blind protein-ligand docking by replica-exchange monte carlo simulation. 37 - Josep Arús-Pous
SMILES-based deep generative scaffold decorator for de-novo drug design. 38 - Ctibor Skuta
QSAR-derived affinity fingerprints (part 1): fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping. 39 - Simon Bray
The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform. 40 - Isidro Cortés-Ciriano
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
One molecular fingerprint to rule them all: drugs, biomolecules, and the metabolome. 43 - Maha A. Thafar
DTiGEMS+: drug-target interaction prediction using graph embedding, graph mining, and similarity-based techniques. 44 - Gerard Baquer
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
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
spyrmsd: symmetry-corrected RMSD calculations in Python. 49 - Tingjun Xu
Neural machine translation of chemical nomenclature between English and Chinese. 50 - A. Patrícia Bento
An open source chemical structure curation pipeline using RDKit. 51 - Ryosuke Shibukawa
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
DeepGraphMolGen, a multi-objective, computational strategy for generating molecules with desirable properties: a graph convolution and reinforcement learning approach. 53 - Simon Bray
Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial. 54 - Jules Leguy
EvoMol: a flexible and interpretable evolutionary algorithm for unbiased de novo molecular generation. 55 - Laurianne David
Molecular representations in AI-driven drug discovery: a review and practical guide. 56 - Pedro Ruas
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
A review of optical chemical structure recognition tools. 60 - Aurelio Antelo-Collado
Maximum common property: a new approach for molecular similarity. 61 - Laeeq Ahmed
Predicting target profiles with confidence as a service using docking scores. 62 - Shunyang Wang
Predicting in silico electron ionization mass spectra using quantum chemistry. 63 - Fernanda I. Saldívar-González
Chemoinformatics-based enumeration of chemical libraries: a tutorial. 64 - Kohulan Rajan
DECIMER: towards deep learning for chemical image recognition. 65 - Gabriel Idakwo, Sundar Thangapandian, Joseph Luttrell IV, Yan Li, Nan Wang, Zhaoxian Zhou
Structure-activity relationship-based chemical classification of highly imbalanced Tox21 datasets. 66 - Jonas Schaub
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
AiZynthFinder: a fast, robust and flexible open-source software for retrosynthetic planning. 70 - Alzbeta Türková
A ligand-based computational drug repurposing pipeline using KNIME and Programmatic Data Access: case studies for rare diseases and COVID-19. 71 - Victorien Delannée
ReactionCode: format for reaction searching, analysis, classification, transform, and encoding/decoding. 72 - Jördis-Ann Schüler
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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