Search Results - "Fourches, Denis"

Inductive transfer learning for molecular activity prediction: Next-Gen QSAR Models with MolPMoFiT by Li, Xinhao, Fourches, Denis

“…Deep neural networks can directly learn from chemical structures without extensive, user-driven selection of descriptors in order to predict molecular…”
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Trust, But Verify: On the Importance of Chemical Structure Curation in Cheminformatics and QSAR Modeling Research by Fourches, Denis, Muratov, Eugene, Tropsha, Alexander

“…Molecular modelers and cheminformaticians typically analyze experimental data generated by other scientists. Consequently, when it comes to data accuracy,…”
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RealityConvert: a tool for preparing 3D models of biochemical structures for augmented and virtual reality by Borrel, Alexandre, Fourches, Denis

“…There is a growing interest for the broad use of Augmented Reality (AR) and Virtual Reality (VR) in the fields of bioinformatics and cheminformatics to…”
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Materials Cartography: Representing and Mining Materials Space Using Structural and Electronic Fingerprints by Isayev, Olexandr, Fourches, Denis, Muratov, Eugene N, Oses, Corey, Rasch, Kevin, Tropsha, Alexander, Curtarolo, Stefano

“…As the proliferation of high-throughput approaches in materials science is increasing the wealth of data in the field, the gap between accumulated-information…”
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QSAR without borders by Muratov, Eugene N, Bajorath, Jürgen, Sheridan, Robert P, Tetko, Igor V, Filimonov, Dmitry, Poroikov, Vladimir, Oprea, Tudor I, Baskin, Igor I, Varnek, Alexandre, Roitberg, Adrian, Isayev, Olexandr, Curtarolo, Stefano, Fourches, Denis, Cohen, Yoram, Aspuru-Guzik, Alan, Winkler, David A, Agrafiotis, Dimitris, Cherkasov, Artem, Tropsha, Alexander

“…Prediction of chemical bioactivity and physical properties has been one of the most important applications of statistical and more recently, machine learning…”
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Quantitative Nanostructure−Activity Relationship Modeling by Fourches, Denis, Pu, Dongqiuye, Tassa, Carlos, Weissleder, Ralph, Shaw, Stanley Y, Mumper, Russell J, Tropsha, Alexander

“…Evaluation of biological effects, both desired and undesired, caused by manufactured nanoparticles (MNPs) is of critical importance for nanotechnology…”
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CERAPP: Collaborative Estrogen Receptor Activity Prediction Project by Mansouri, Kamel, Abdelaziz, Ahmed, Rybacka, Aleksandra, Roncaglioni, Alessandra, Tropsha, Alexander, Varnek, Alexandre, Zakharov, Alexey, Worth, Andrew, Richard, Ann M, Grulke, Christopher M, Trisciuzzi, Daniela, Fourches, Denis, Horvath, Dragos, Benfenati, Emilio, Muratov, Eugene, Wedebye, Eva Bay, Grisoni, Francesca, Mangiatordi, Giuseppe F, Incisivo, Giuseppina M, Hong, Huixiao, Ng, Hui W, Tetko, Igor V, Balabin, Ilya, Kancherla, Jayaram, Shen, Jie, Burton, Julien, Nicklaus, Marc, Cassotti, Matteo, Nikolov, Nikolai G, Nicolotti, Orazio, Andersson, Patrik L, Zang, Qingda, Politi, Regina, Beger, Richard D, Todeschini, Roberto, Huang, Ruili, Farag, Sherif, Rosenberg, Sine A, Slavov, Svetoslav, Hu, Xin, Judson, Richard S

“…Humans are exposed to thousands of man-made chemicals in the environment. Some chemicals mimic natural endocrine hormones and, thus, have the potential to be…”
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Comprehensive characterization of the Published Kinase Inhibitor Set by Elkins, Jonathan M, Fedele, Vita, Szklarz, Marta, Abdul Azeez, Kamal R, Salah, Eidarus, Mikolajczyk, Jowita, Romanov, Sergei, Sepetov, Nikolai, Huang, Xi-Ping, Roth, Bryan L, Al Haj Zen, Ayman, Fourches, Denis, Muratov, Eugene, Tropsha, Alex, Morris, Joel, Teicher, Beverly A, Kunkel, Mark, Polley, Eric, Lackey, Karen E, Atkinson, Francis L, Overington, John P, Bamborough, Paul, Müller, Susanne, Price, Daniel J, Willson, Timothy M, Drewry, David H, Knapp, Stefan, Zuercher, William J

“…A well-characterized library of experimental kinase inhibitors provides leads for targeting the untargeted kinome. Despite the success of protein kinase…”
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Ion mobility spectrometry and the omics: Distinguishing isomers, molecular classes and contaminant ions in complex samples by Burnum-Johnson, Kristin E., Zheng, Xueyun, Dodds, James N., Ash, Jeremy, Fourches, Denis, Nicora, Carrie D., Wendler, Jason P., Metz, Thomas O., Waters, Katrina M., Jansson, Janet K., Smith, Richard D., Baker, Erin S.

“…Ion mobility spectrometry (IMS) is a widely used analytical technique providing rapid gas phase separations. IMS alone is useful, but its coupling with mass…”
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Predicting Drug-Induced Hepatotoxicity Using QSAR and Toxicogenomics Approaches by Low, Yen, Uehara, Takeki, Minowa, Yohsuke, Yamada, Hiroshi, Ohno, Yasuo, Urushidani, Tetsuro, Sedykh, Alexander, Muratov, Eugene, Kuz’min, Viktor, Fourches, Denis, Zhu, Hao, Rusyn, Ivan, Tropsha, Alexander

“…Quantitative structure–activity relationship (QSAR) modeling and toxicogenomics are typically used independently as predictive tools in toxicology. In this…”
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Pred-hERG: A Novel web-Accessible Computational Tool for Predicting Cardiac Toxicity by Braga, Rodolpho C., Alves, Vinicius M., Silva, Meryck F. B., Muratov, Eugene, Fourches, Denis, Lião, Luciano M., Tropsha, Alexander, Andrade, Carolina H.

“…The blockage of the hERG K+ channels is closely associated with lethal cardiac arrhythmia. The notorious ligand promiscuity of this channel earmarked hERG as…”
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Critical Assessment of QSAR Models of Environmental Toxicity against Tetrahymena pyriformis: Focusing on Applicability Domain and Overfitting by Variable Selection by Tetko, Igor V, Sushko, Iurii, Pandey, Anil Kumar, Zhu, Hao, Tropsha, Alexander, Papa, Ester, Öberg, Tomas, Todeschini, Roberto, Fourches, Denis, Varnek, Alexandre

“…The estimation of the accuracy of predictions is a critical problem in QSAR modeling. The “distance to model” can be defined as a metric that defines the…”
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Exploring quantitative nanostructure-activity relationships (QNAR) modeling as a tool for predicting biological effects of manufactured nanoparticles by Fourches, Denis, Pu, Dongqiuye, Tropsha, Alexander

“…Evaluation of desired and undesired, biological effects of Manufactured NanoParticles (MNPs) is of critical importance for the future of nanotechnology…”
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SIME: synthetic insight-based macrolide enumerator to generate the V1B library of 1 billion macrolides by Zin, Phyo Phyo Kyaw, Williams, Gavin, Fourches, Denis

“…We report on a new cheminformatics enumeration technology—SIME, synthetic insight-based macrolide enumerator—a new and improved software technology. SIME can…”
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Tuning HERG out: antitarget QSAR models for drug development by Braga, Rodolpho C, Alves, Vinicius M, Silva, Meryck F B, Muratov, Eugene, Fourches, Denis, Tropsha, Alexander, Andrade, Carolina H

“…Several non-cardiovascular drugs have been withdrawn from the market due to their inhibition of hERG K+ channels that can potentially lead to severe heart…”
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Combinatorial QSAR modeling of chemical toxicants tested against Tetrahymena pyriformis by Zhu, Hao, Tropsha, Alexander, Fourches, Denis, Varnek, Alexandre, Papa, Ester, Gramatica, Paola, Oberg, Tomas, Dao, Phuong, Cherkasov, Artem, Tetko, Igor V

“…Selecting most rigorous quantitative structure-activity relationship (QSAR) approaches is of great importance in the development of robust and predictive…”
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Predicting chemically-induced skin reactions. Part II: QSAR models of skin permeability and the relationships between skin permeability and skin sensitization by Alves, Vinicius M., Muratov, Eugene, Fourches, Denis, Strickland, Judy, Kleinstreuer, Nicole, Andrade, Carolina H., Tropsha, Alexander

“…Skin permeability is widely considered to be mechanistically implicated in chemically-induced skin sensitization. Although many chemicals have been identified…”
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Target-Specific Native/Decoy Pose Classifier Improves the Accuracy of Ligand Ranking in the CSAR 2013 Benchmark by Fourches, Denis, Politi, Regina, Tropsha, Alexander

“…As part of the CSAR 2013 benchmark exercise, we have implemented a hybrid docking and scoring workflow to rank 10 steroid ligands of an engineered…”
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Applicability Domains for Classification Problems: Benchmarking of Distance to Models for Ames Mutagenicity Set by Sushko, Iurii, Novotarskyi, Sergii, Körner, Robert, Pandey, Anil Kumar, Cherkasov, Artem, Li, Jiazhong, Gramatica, Paola, Hansen, Katja, Schroeter, Timon, Müller, Klaus-Robert, Xi, Lili, Liu, Huanxiang, Yao, Xiaojun, Öberg, Tomas, Hormozdiari, Farhad, Dao, Phuong, Sahinalp, Cenk, Todeschini, Roberto, Polishchuk, Pavel, Artemenko, Anatoliy, Kuz’min, Victor, Martin, Todd M, Young, Douglas M, Fourches, Denis, Muratov, Eugene, Tropsha, Alexander, Baskin, Igor, Horvath, Dragos, Marcou, Gilles, Muller, Christophe, Varnek, Alexander, Prokopenko, Volodymyr V, Tetko, Igor V

“…The estimation of accuracy and applicability of QSAR and QSPR models for biological and physicochemical properties represents a critical problem. The developed…”
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In vitro and in vivo Evaluation of in silico Predicted Pneumococcal UDPG:PP Inhibitors by Cools, Freya, Triki, Dhoha, Geerts, Nele, Delputte, Peter, Fourches, Denis, Cos, Paul

“…Pneumonia, of which Streptococcus pneumoniae is the most common causative agent, is considered one of the three top leading causes of death worldwide. As seen…”
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