Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model von Wang, Sheng, Sun, Siqi, Li, Zhen, Zhang, Renyu, Xu, Jinbo

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Propagating annotations of molecular networks using in silico fragmentation von da Silva, Ricardo R, Wang, Mingxun, Nothias, Louis-Félix, van der Hooft, Justin J J, Caraballo-Rodríguez, Andrés Mauricio, Fox, Evan, Balunas, Marcy J, Klassen, Jonathan L, Lopes, Norberto Peporine, Dorrestein, Pieter C

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TranSynergy: Mechanism-driven interpretable deep neural network for the synergistic prediction and pathway deconvolution of drug combinations von Liu, Qiao, Xie, Lei

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iDrug: Integration of drug repositioning and drug-target prediction via cross-network embedding von Chen, Huiyuan, Cheng, Feixiong, Li, Jing

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Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes von Upadhyay, Amit A, Fleetwood, Aaron D, Adebali, Ogun, Finn, Robert D, Zhulin, Igor B

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A novel virtual screening procedure identifies Pralatrexate as inhibitor of SARS-CoV-2 RdRp and it reduces viral replication in vitro von Zhang, Haiping, Yang, Yang, Li, Junxin, Wang, Min, Saravanan, Konda Mani, Wei, Jinli, Ng, Justin Tze-Yang, Hossain, Md Tofazzal, Liu, Maoxuan, Zhang, Huiling, Ren, Xiaohu, Pan, Yi, Peng, Yin, Shi, Yi, Wan, Xiaochun, Liu, Yingxia, Wei, Yanjie

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Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors von Cichonska, Anna, Ravikumar, Balaguru, Parri, Elina, Timonen, Sanna, Pahikkala, Tapio, Airola, Antti, Wennerberg, Krister, Rousu, Juho, Aittokallio, Tero

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Transfer learning enables prediction of CYP2D6 haplotype function von McInnes, Gregory, Dalton, Rachel, Sangkuhl, Katrin, Whirl-Carrillo, Michelle, Lee, Seung-Been, Tsao, Philip S., Gaedigk, Andrea, Altman, Russ B., Woodahl, Erica L.

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Machine learning-driven identification of drugs inhibiting cytochrome P450 2C9 von Goldwaser, Elodie, Laurent, Catherine, Lagarde, Nathalie, Fabrega, Sylvie, Nay, Laure, Villoutreix, Bruno O, Jelsch, Christian, Nicot, Arnaud B, Loriot, Marie-Anne, Miteva, Maria A

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Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models? von Kapla, Jon, Rodriguez Espigares, Ismael, Ballante, Flavio, Selent, Jana, Carlsson, Jens

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Tissue-guided LASSO for prediction of clinical drug response using preclinical samples von Huang, Edward W., Bhope, Ameya, Lim, Jing, Sinha, Saurabh, Emad, Amin

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Evaluation of residue-residue contact prediction methods: From retrospective to prospective von Zhang, Huiling, Bei, Zhendong, Xi, Wenhui, Hao, Min, Ju, Zhen, Saravanan, Konda Mani, Zhang, Haiping, Guo, Ning, Wei, Yanjie

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Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing von Lim, Hansaim, Poleksic, Aleksandar, Yao, Yuan, Tong, Hanghang, He, Di, Zhuang, Luke, Meng, Patrick, Xie, Lei

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Predicting protein targets for drug-like compounds using transcriptomics von Pabon, Nicolas A, Xia, Yan, Estabrooks, Samuel K, Ye, Zhaofeng, Herbrand, Amanda K, Süß, Evelyn, Biondi, Ricardo M, Assimon, Victoria A, Gestwicki, Jason E, Brodsky, Jeffrey L, Camacho, Carlos J, Bar-Joseph, Ziv

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Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2 von Dwivedy, Abhisek, Mariadasse, Richard, Ahmad, Mohammed, Chakraborty, Sayan, Kar, Deepsikha, Tiwari, Satish, Bhattacharyya, Sankar, Sonar, Sudipta, Mani, Shailendra, Tailor, Prafullakumar, Majumdar, Tanmay, Jeyakanthan, Jeyaraman, Biswal, Bichitra Kumar

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GCSENet: A GCN, CNN and SENet ensemble model for microRNA-disease association prediction von Li, Zhong, Jiang, Kaiyancheng, Qin, Shengwei, Zhong, Yijun, Elofsson, Arne

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ATRPred: A machine learning based tool for clinical decision making of anti-TNF treatment in rheumatoid arthritis patients von Prasad, Bodhayan, McGeough, Cathy, Eakin, Amanda, Ahmed, Tan, Small, Dawn, Gardiner, Philip, Pendleton, Adrian, Wright, Gary, Bjourson, Anthony J, Gibson, David S, Shukla, Priyank

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Full scale structural, mechanical and dynamical properties of HIV-1 liposomes von Bryer, Alexander J, Reddy, Tyler, Lyman, Edward, Perilla, Juan R

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Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach von Espinoza, Josh L., Dupont, Chris L., O'Rourke, Aubrie, Beyhan, Sinem, Morales, Pavel, Spoering, Amy, Meyer, Kirsten J., Chan, Agnes P., Choi, Yongwook, Nierman, William C., Lewis, Kim, Nelson, Karen E.

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A kinetic mechanism for enhanced selectivity of membrane transport von Bisignano, Paola, Lee, Michael A., George, August, Zuckerman, Daniel M., Grabe, Michael, Rosenberg, John M.

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