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Predicting S. aureus antimicrobial resistance with interpretable genomic space maps Mol. Inform. (IF 3.6) Pub Date : 2024-02-22 Karina Pikalyova, Alexey Orlov, Dragos Horvath, Gilles Marcou, Alexandre Varnek
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Application of machine learning-based read-across structure-property relationship (RASPR) as a new tool for predictive modelling: Prediction of power conversion efficiency (PCE) for selected classes of organic dyes in dye-sensitized solar cells (DSSCs) Mol. Inform. (IF 3.6) Pub Date : 2024-02-19 Souvik Pore, Arkaprava Banerjee, Kunal Roy
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An ensemble-based approach to estimate confidence of predicted protein–ligand binding affinity values Mol. Inform. (IF 3.6) Pub Date : 2024-02-15 Milad Rayka, Morteza Mirzaei, Ali Mohammad Latifi
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The macrocycle inhibitor landscape of SLC-transporter Mol. Inform. (IF 3.6) Pub Date : 2024-01-30 Nejra Granulo, Sergey Sosnin, Daniela Digles, Gerhard F. Ecker
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Synthetically accessible de novo design using reaction vectors: Application to PARP1 inhibitors** Mol. Inform. (IF 3.6) Pub Date : 2024-01-22 Gian Marco Ghiandoni, Stuart R. Flanagan, Michael J. Bodkin, Maria Giulia Nizi, Albert Galera-Prat, Annalaura Brai, Beining Chen, James E. A. Wallace, Dimitar Hristozov, James Webster, Giuseppe Manfroni, Lari Lehtiö, Oriana Tabarrini, Valerie J. Gillet
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In Silico prediction of inhibitors for multiple transporters via machine learning methods Mol. Inform. (IF 3.6) Pub Date : 2024-01-18 Hao Duan, Chaofeng Lou, Yaxin Gu, Yimeng Wang, Weihua Li, Guixia Liu, Yun Tang
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In silico construction of a focused fragment library facilitating exploration of chemical space** Mol. Inform. (IF 3.6) Pub Date : 2024-01-09 Weijie Han, Xiaohe Xu, Qing Fan, Yingchao Yan, YanMin Zhang, Yadong Chen, Haichun Liu
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Exploring data-driven chemical SMILES tokenization approaches to identify key protein–ligand binding moieties Mol. Inform. (IF 3.6) Pub Date : 2024-01-09 Asu Busra Temizer, Gökçe Uludoğan, Rıza Özçelik, Taha Koulani, Elif Ozkirimli, Kutlu O. Ulgen, Nilgun Karali, Arzucan Özgür
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Automatic generation of functional peptides with desired bioactivity and membrane permeability using Bayesian optimization Mol. Inform. (IF 3.6) Pub Date : 2024-01-05 Itsuki Fukunaga, Yuki Matsukiyo, Kazuma Kaitoh, Yoshihiro Yamanishi
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Kinetic solubility: Experimental and machine-learning modeling perspectives Mol. Inform. (IF 3.6) Pub Date : 2023-12-27 Shamkhal Baybekov, Pierre Llompart, Gilles Marcou, Patrick Gizzi, Jean-Luc Galzi, Pascal Ramos, Olivier Saurel, Claire Bourban, Claire Minoletti, Alexandre Varnek
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Targeting of essential mycobacterial replication enzyme DnaG primase revealed Mitoxantrone and Vapreotide as novel mycobacterial growth inhibitors** Mol. Inform. (IF 3.6) Pub Date : 2023-12-20 Waseem Ali, Salma Jamal, Rishabh Gangwar, Faraz Ahmed, Rahul Sharma, Meetu Agarwal, Javaid Ahmad Sheikh, Abhinav Grover, Sonam Grover
Tuberculosis (TB) is the second leading cause of mortality after COVID-19, with a global death toll of 1.6 million in 2021. The escalating situation of drug-resistant forms of TB has threatened the current TB management strategies. New therapeutics with novel mechanisms of action are urgently required to address the current global TB crisis. The essential mycobacterial primase DnaG with no structural
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Similarity searching for anticandidal agents employing a repurposing approach Mol. Inform. (IF 3.6) Pub Date : 2023-12-14 Karen Rodríguez-Villar, Francisco Cortés-Benítez, Juan Francisco Palacios-Espinosa, Jaime Pérez-Villanueva
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Predicting the bandgap and efficiency of perovskite solar cells using machine learning methods Mol. Inform. (IF 3.6) Pub Date : 2023-12-05 Asad Khan, Jeevan Kandel, Hilal Tayara, Kil To Chong
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CIPSI: An open chemical intellectual property service for medicinal chemists Mol. Inform. (IF 3.6) Pub Date : 2023-11-27 Maria Martinez-Sevillano, Maria J. Falaguera, Jordi Mestres
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Chemical language models for molecular design Mol. Inform. (IF 3.6) Pub Date : 2023-11-27 Jürgen Bajorath
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Integrated workflow for the identification of new GABAAR positive allosteric modulators based on the in silico screening with further in vitro validation. Case study using Enamine's stock chemical space Mol. Inform. (IF 3.6) Pub Date : 2023-11-14 Maksym Platonov, Oleksandr Maximyuk, Alexey Rayevsky, Olena Iegorova, Vasyl Hurmach, Yuliia Holota, Elijah Bulgakov, Andrii Cherninskyi, Pavel Karpov, Sergey Ryabukhin, Oleg Krishtal, Dmitriy Volochnyuk
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Classification of tastants: A deep learning based approach Mol. Inform. (IF 3.6) Pub Date : 2023-10-26 Prantar Dutta, Deepak Jain, Rakesh Gupta, Beena Rai
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GUIDEMOL: A Python graphical user interface for molecular descriptors based on RDKit Mol. Inform. (IF 3.6) Pub Date : 2023-10-26 Joao Aires-de-Sousa
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Predicting the duration of action of β2-adrenergic receptor agonists: Ligand and structure-based approaches Mol. Inform. (IF 3.6) Pub Date : 2023-10-23 Luca Chiesa, Emilie Sick, Esther Kellenberger
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A community effort in SARS-CoV-2 drug discovery Mol. Inform. (IF 3.6) Pub Date : 2023-10-13 Johannes Schimunek, Philipp Seidl, Katarina Elez, Tim Hempel, Tuan Le, Frank Noé, Simon Olsson, Lluís Raich, Robin Winter, Hatice Gokcan, Filipp Gusev, Evgeny M. Gutkin, Olexandr Isayev, Maria G. Kurnikova, Chamali H. Narangoda, Roman Zubatyuk, Ivan P. Bosko, Konstantin V. Furs, Anna D. Karpenko, Yury V. Kornoushenko, Mikita Shuldau, Artsemi Yushkevich, Mohammed B. Benabderrahmane, Patrick Bousquet-Melou
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HIt Discovery using docking ENriched by GEnerative Modeling (HIDDEN GEM): A novel computational workflow for accelerated virtual screening of ultra-large chemical libraries Mol. Inform. (IF 3.6) Pub Date : 2023-10-06 Konstantin I. Popov, James Wellnitz, Travis Maxfield, Alexander Tropsha
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An in silico investigation of Kv2.1 potassium channel: Model building and inhibitors binding sites analysis** Mol. Inform. (IF 3.6) Pub Date : 2023-10-04 Xiaoyu Wang, Xinyuan Zhang, Jie Zhou, Weiping Wang, Xiaoliang Wang, Bailing Xu
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AliNA – a deep learning program for RNA secondary structure prediction Mol. Inform. (IF 3.6) Pub Date : 2023-09-14 Shamsudin S. Nasaev, Artem R. Mukanov, Ivan I. Kuznetsov, Alexander V. Veselovsky
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Use of tree-based machine learning methods to screen affinitive peptides based on docking data Mol. Inform. (IF 3.6) Pub Date : 2023-09-11 Hua Feng, Fangyu Wang, Ning Li, Qian Xu, Guanming Zheng, Xuefeng Sun, Man Hu, Xuewu Li, Guangxu Xing, Gaiping Zhang
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Data-driven approaches for identifying hyperparameters in multi-step retrosynthesis Mol. Inform. (IF 3.6) Pub Date : 2023-09-07 Annie M. Westerlund, Bente Barge, Lewis Mervin, Samuel Genheden
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Cell-penetrating peptides predictors: A comparative analysis of methods and datasets Mol. Inform. (IF 3.6) Pub Date : 2023-09-06 Karen Guerrero-Vázquez, Gabriel Del Rio, Carlos A. Brizuela
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Development of novel ligands against SARS-CoV-2 Mpro enzyme: an in silico and in vitro Study Mol. Inform. (IF 3.6) Pub Date : 2023-08-17 Navid Kaboudi, Nadine Krüger, Maryam Hamzeh-Mivehroud
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A multi-tier computational screening framework to effectively search the mutational space of SARS-CoV-2 receptor binding motif to identify mutants with enhanced ACE2 binding abilities Mol. Inform. (IF 3.6) Pub Date : 2023-08-17 Sandipan Chakraborty, Chiranjeet Saha
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Absorption matters: A closer look at popular oral bioavailability rules for drug approvals Mol. Inform. (IF 3.6) Pub Date : 2023-08-07 Artur Caminero Gomes Soares, Gustavo Henrique Marques Sousa, Raisa Ludmila Calil, Gustavo Henrique Goulart Trossini
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Phenothiazine-based virtual screening, molecular docking, and molecular dynamics of new trypanothione reductase inhibitors of Trypanosoma cruzi Mol. Inform. (IF 3.6) Pub Date : 2023-07-25 Alonzo González-González, Citlali Vázquez, Rusely Encalada, Emma Saavedra, Lenci K. Vázquez-Jiménez, Eyra Ortiz-Pérez, María Laura Bolognesi, Gildardo Rivera
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Conjugated quantitative structure-property relationship models: Prediction of kinetic characteristics linked by the Arrhenius equation Mol. Inform. (IF 3.6) Pub Date : 2023-07-24 Dmitry Zankov, Timur Madzhidov, Igor Baskin, Alexandre Varnek
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De novo drug design based on patient gene expression profiles via deep learning Mol. Inform. (IF 3.6) Pub Date : 2023-07-20 Chikashige Yamanaka, Shunya Uki, Kazuma Kaitoh, Michio Iwata, Yoshihiro Yamanishi
1 INTRODUCTION The development of new drugs is enormously costly. It typically takes 10–15 years and billions of dollars to develop and market a drug 1, 2. One of the most challenging tasks in the drug discovery process is the identification of hits. One factor is the size of the chemical space since there are theoretically 1023–1060 drug-like molecules 3-5. Hit identification requires the discovery
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Natural-Language Processing (NLP) based feature extraction technique in Deep-Learning model to predict the Blood-Brain-Barrier permeability of molecules Mol. Inform. (IF 3.6) Pub Date : 2023-07-04 Ravi Singh, Powsali Ghosh, Ankit Ganeshpurkar, Asha Anand, Rayala Swetha, Ravi Bhushan Singh, Dileep Kumar, Sushil Kumar Singh, Ashok Kumar
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Computer-aided design of muscarinic acetylcholine receptor M3 inhibitors: Promising compounds among trifluoromethyl containing hexahydropyrimidinones/thiones Mol. Inform. (IF 3.6) Pub Date : 2023-06-09 Alex Nyporko, Olga Tsymbalyuk, Ivan Voiteshenko, Sergiy Starosyla, Mykola Protopopov, Volodymyr Bdzhola
Conflict of interest None declared.
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Deimos: A novel automated methodology for optimal grouping. Application to nanoinformatics case studies Mol. Inform. (IF 3.6) Pub Date : 2023-05-31 Dimitra-Danai Varsou, Haralambos Sarimveis
Conflict of interest The authors declare no potential conflict of interests.
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Augmenting bioactivity by docking-generated multiple ligand poses to enhance machine learning and pharmacophore modelling: discovery of new TTK inhibitors as case study Mol. Inform. (IF 3.6) Pub Date : 2023-05-24 Amenah M. AL-Imam, Safa Daoud, Ma'mon M. Hatmal, Mutasem Omar Taha
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Feature importance-based interpretation of UMAP-visualized polymer space Mol. Inform. (IF 3.6) Pub Date : 2023-05-22 Takuya Ehiro
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Exploring activity landscapes with extended similarity: is Tanimoto enough? Mol. Inform. (IF 3.6) Pub Date : 2023-05-18 Timothy B. Dunn, Edgar López-López, Taewon David Kim, José L. Medina-Franco, Ramón Alain Miranda-Quintana
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In silico prediction of drug-induced liver injury with a complementary integration strategy based on hybrid representation Mol. Inform. (IF 3.6) Pub Date : 2023-05-17 Yaxin Gu, Yimeng Wang, Zengrui Wu, Weihua Li, Guixia Liu, Yun Tang
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The VEGA web service: multipurpose online tools for molecular modelling and docking analyses Mol. Inform. (IF 3.6) Pub Date : 2023-05-16 Alessandro Pedretti, Serena Vittorio, Emanuela Sabato, Giulio Vistoli, Angelica Mazzolari
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Novel Inhibitors of androgen receptor's DNA binding domain identified using an ultra-large virtual screening Mol. Inform. (IF 3.6) Pub Date : 2023-05-16 Mariia Radaeva, Helene Morin, Mohit Pandey, Fuqiang Ban, Maria Guo, Eric LeBlanc, Nada Lallous, Artem Cherkasov
1 INTRODUCTION Androgen receptor is the main driver of prostate cancer (PCa) (the most common malignancy in men), as it activates the transcription of a variety of oncogenes and stimulates cancer cell growth 1. The inhibition of AR with small molecules that compete with natural androgens is one of the primary strategies in PC therapy along with androgen synthesis ablation through castration 2. However
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Application of automated machine learning in the identification of multi-target-directed ligands blocking PDE4B, PDE8A, and TRPA1 with potential use in the treatment of asthma and COPD Mol. Inform. (IF 3.6) Pub Date : 2023-05-16 Alicja Gawalska, Natalia Czub, Michał Sapa, Marcin Kołaczkowski, Adam Bucki, Aleksander Mendyk
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Compression of molecular fingerprints with autoencoder networks Mol. Inform. (IF 3.6) Pub Date : 2023-05-10 Agnieszka Ilnicka, Gisbert Schneider
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Gas-to-ionic liquid partition: QSPR modeling and mechanistic interpretation Mol. Inform. (IF 3.6) Pub Date : 2023-04-11 Jia-Xi Chang, Jian-Wei Zou, Chao-Yuan Lou, Jia-Xin Ye, Rui Feng, Zi-Yuan Li, Gui-Xiang Hu
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Comparison of deep learning models with simple method to assess the problem of antimicrobial peptides prediction Mol. Inform. (IF 3.6) Pub Date : 2023-03-24 M. Y. Lobanov, M. V. Slizen, N. V. Dovidchenko, A. V. Panfilov, A. A. Surin, I. V. Likhachev, O. V. Galzitskaya
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Identification of a PD1/PD-L1 inhibitor by structure-based pharmacophore modelling, virtual screening, molecular docking and biological evaluation** Mol. Inform. (IF 3.6) Pub Date : 2023-03-10 Anju Choorakottayil Pushkaran, Kumaran K, Ann Maria T, Raja Biswas, C. Gopi Mohan
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Overproduce and select, or determine optimal molecular descriptor subset via configuration space optimization? Application to the prediction of ecotoxicological endpoints Mol. Inform. (IF 3.6) Pub Date : 2023-03-09 Luis A. García-González, Yovani Marrero-Ponce, Carlos A. Brizuela, César R. García-Jacas
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A new set of KNIME nodes implementing the QPhAR algorithm Mol. Inform. (IF 3.6) Pub Date : 2023-03-05 Stefan M. Kohlbacher, Gökhan Ibis, Christian Permann, Sharon Bryant, Thierry Langer, Thomas Seidel
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Fragment-based deep molecular generation using hierarchical chemical graph representation and multi-resolution graph variational autoencoder Mol. Inform. (IF 3.6) Pub Date : 2023-02-10 Zhenxiang Gao, Xinyu Wang, Blake Blumenfeld Gaines, Xuetao Shi, Jinbo Bi, Minghu Song
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Discovery of natural-derived Mpro inhibitors as therapeutic candidates for COVID-19: Structure-based pharmacophore screening combined with QSAR analysis Mol. Inform. (IF 3.6) Pub Date : 2023-02-10 Mohammad A. Khanfar, Nada Salaas, Reem Abumostafa
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Co-model for chemical toxicity prediction based on multi-task deep learning Mol. Inform. (IF 3.6) Pub Date : 2023-02-01 Yuan Yuan Li, Lingfeng Chen, Chengtao Pu, Chengdong Zang, YingChao Yan, Yadong Chen, Yanmin Zhang, Haichun Liu
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GB-score: Minimally designed machine learning scoring function based on distance-weighted interatomic contact features Mol. Inform. (IF 3.6) Pub Date : 2023-02-01 Milad Rayka, Rohoullah Firouzi
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Exploring cooperative molecular contacts using a PostgreSQL database system Mol. Inform. (IF 3.6) Pub Date : 2023-01-18 Mael A. Briand, Loïc Dreano, Ashenafi Legehar, Evgeni Grazhdankin, Léo Ghemtio, Henri Xhaard
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Exploring isofunctional molecules: Design of a benchmark and evaluation of prediction performance Mol. Inform. (IF 3.6) Pub Date : 2023-01-12 Philippe Pinel, Gwenn Guichaoua, Matthieu Najm, Stéphanie Labouille, Nicolas Drizard, Yann Gaston-Mathé, Brice Hoffmann, Véronique Stoven
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A machine learning q-RASPR approach for efficient predictions of the specific surface area of perovskites** Mol. Inform. (IF 3.6) Pub Date : 2023-01-08 Arkaprava Banerjee, Agnieszka Gajewicz-Skretna, Kunal Roy
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A comparison between 2D and 3D descriptors in QSAR modeling based on bio-active conformations Mol. Inform. (IF 3.6) Pub Date : 2023-01-08 Malkeet Singh Bahia, Omer Kaspi, Meir Touitou, Idan Binayev, Seema Dhail, Jacob Spiegel, Netaly Khazanov, Abraham Yosipof, Hanoch Senderowitz
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French dispatch: GTM-based analysis of the Chimiothèque Nationale Chemical Space Mol. Inform. (IF 3.6) Pub Date : 2023-01-05 Polina Oleneva, Yuliana Zabolotna, Dragos Horvath, Gilles Marcou, Fanny Bonachera, Alexandre Varnek
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Automated detection of toxicophores and prediction of mutagenicity using PMCSFG algorithm Mol. Inform. (IF 3.6) Pub Date : 2022-12-18 Leander Schietgat, Bertrand Cuissart, Kurt De Grave, Kyriakos Efthymiadis, Ronan Bureau, Bruno Crémilleux, Jan Ramon, Alban Lepailleur
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Artificial neural network models driven novel virtual screening workflow for the identification and biological evaluation of BACE1 inhibitors Mol. Inform. (IF 3.6) Pub Date : 2022-12-02 Kushagra Kashyap, Lalita Panigrahi, Shakil Ahmed, Mohammad Imran Siddiqi