Search Results - "Lyu, Jiankun"

A practical guide to large-scale docking by Bender, Brian J., Gahbauer, Stefan, Luttens, Andreas, Lyu, Jiankun, Webb, Chase M., Stein, Reed M., Fink, Elissa A., Balius, Trent E., Carlsson, Jens, Irwin, John J., Shoichet, Brian K.

“…Structure-based docking screens of large compound libraries have become common in early drug and probe discovery. As computer efficiency has improved and…”
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Ultra-large library docking for discovering new chemotypes by Lyu, Jiankun, Wang, Sheng, Balius, Trent E., Singh, Isha, Levit, Anat, Moroz, Yurii S., O’Meara, Matthew J., Che, Tao, Algaa, Enkhjargal, Tolmachova, Kateryna, Tolmachev, Andrey A., Shoichet, Brian K., Roth, Bryan L., Irwin, John J.

“…Despite intense interest in expanding chemical space, libraries containing hundreds-of-millions to billions of diverse molecules have remained inaccessible…”
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Structure of a Hallucinogen-Activated Gq-Coupled 5-HT2A Serotonin Receptor by Kim, Kuglae, Che, Tao, Panova, Ouliana, DiBerto, Jeffrey F., Lyu, Jiankun, Krumm, Brian E., Wacker, Daniel, Robertson, Michael J., Seven, Alpay B., Nichols, David E., Shoichet, Brian K., Skiniotis, Georgios, Roth, Bryan L.

“…Hallucinogens like lysergic acid diethylamide (LSD), psilocybin, and substituted N-benzyl phenylalkylamines are widely used recreationally with psilocybin…”
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Drug-induced phospholipidosis confounds drug repurposing for SARS-CoV-2 by Tummino, Tia A, Rezelj, Veronica V, Fischer, Benoit, Fischer, Audrey, O'Meara, Matthew J, Monel, Blandine, Vallet, Thomas, White, Kris M, Zhang, Ziyang, Alon, Assaf, Schadt, Heiko, O'Donnell, Henry R, Lyu, Jiankun, Rosales, Romel, McGovern, Briana L, Rathnasinghe, Raveen, Jangra, Sonia, Schotsaert, Michael, Galarneau, Jean-René, Krogan, Nevan J, Urban, Laszlo, Shokat, Kevan M, Kruse, Andrew C, García-Sastre, Adolfo, Schwartz, Olivier, Moretti, Francesca, Vignuzzi, Marco, Pognan, Francois, Shoichet, Brian K

“…Repurposing drugs as treatments for COVID-19, the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has drawn much attention…”
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Structures of the σ2 receptor enable docking for bioactive ligand discovery by Alon, Assaf, Lyu, Jiankun, Braz, Joao M., Tummino, Tia A., Craik, Veronica, O’Meara, Matthew J., Webb, Chase M., Radchenko, Dmytro S., Moroz, Yurii S., Huang, Xi-Ping, Liu, Yongfeng, Roth, Bryan L., Irwin, John J., Basbaum, Allan I., Shoichet, Brian K., Kruse, Andrew C.

“…The σ 2 receptor has attracted intense interest in cancer imaging 1 , psychiatric disease 2 , neuropathic pain 3 – 5 and other areas of biology 6 , 7 . Here we…”
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Design, Synthesis, and Biological Evaluation of Pyrimido[4,5‑d]pyrimidine-2,4(1H,3H)‑diones as Potent and Selective Epidermal Growth Factor Receptor (EGFR) Inhibitors against L858R/T790M Resistance Mutation by Hao, Yongjia, Lyu, Jiankun, Qu, Rong, Tong, Yi, Sun, Deheng, Feng, Fang, Tong, Linjiang, Yang, Tingyuan, Zhao, Zhenjiang, Zhu, Lili, Ding, Jian, Xu, Yufang, Xie, Hua, Li, Honglin

“…First-generation epidermal growth factor receptor (EGFR) inhibitors, gefitinib and erlotinib, have achieved initially marked clinical efficacy for nonsmall…”
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Publisher Correction: A practical guide to large-scale docking by Bender, Brian J., Gahbauer, Stefan, Luttens, Andreas, Lyu, Jiankun, Webb, Chase M., Stein, Reed M., Fink, Elissa A., Balius, Trent E., Carlsson, Jens, Irwin, John J., Shoichet, Brian K.

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Structure-Guided Design of C4-alkyl-1,4-dihydro-2H-pyrimido[4,5-d][1,3]oxazin-2-ones as Potent and Mutant-Selective Epidermal Growth Factor Receptor (EGFR) L858R/T790M Inhibitors by Hao, Yongjia, Lyu, Jiankun, Qu, Rong, Sun, Deheng, Zhao, Zhenjiang, Chen, Zhuo, Ding, Jian, Xie, Hua, Xu, Yufang, Li, Honglin

“…Epidermal growth factor receptor (EGFR) T790M acquired drug-resistance mutation has become a major clinical challenge for the therapy of non-small cell lung…”
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Antiproliferative and apoptosis-inducing activities of novel naphthalimide–cyclam conjugates through dual topoisomerase (topo) I/II inhibition by Tan, Shaoying, Sun, Deheng, Lyu, Jiankun, Sun, Xiao, Wu, Fangshu, Li, Qiang, Yang, Yiqi, Liu, Jianxu, Wang, Xin, Chen, Zhuo, Li, Honglin, Qian, Xuhong, Xu, Yufang

“…A novel series of naphthalimide–cyclam compounds were designed and synthesized. They were evaluated of their antiproliferative and apoptosis-inducing…”
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Modeling the expansion of virtual screening libraries by Lyu, Jiankun, Irwin, John J., Shoichet, Brian K.

“…Recently, ‘tangible’ virtual libraries have made billions of molecules readily available. Prioritizing these molecules for synthesis and testing demands…”
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A SARS-CoV-2 protein interaction map reveals targets for drug repurposing by Gordon, David E., Jang, Gwendolyn M., Bouhaddou, Mehdi, Xu, Jiewei, Obernier, Kirsten, White, Kris M., O’Meara, Matthew J., Rezelj, Veronica V., Guo, Jeffrey Z., Swaney, Danielle L., Tummino, Tia A., Kaake, Robyn M., Richards, Alicia L., Tutuncuoglu, Beril, Foussard, Helene, Haas, Kelsey, Modak, Maya, Haas, Paige, Braberg, Hannes, Fabius, Jacqueline M., Eckhardt, Manon, Bennett, Melanie J., Cakir, Merve, McGregor, Michael J., Li, Qiongyu, Roesch, Ferdinand, Vallet, Thomas, Mac Kain, Alice, Miorin, Lisa, Moreno, Elena, Naing, Zun Zar Chi, Zhou, Yuan, Peng, Shiming, Shi, Ying, Zhang, Ziyang, Shen, Wenqi, Kirby, Ilsa T., Melnyk, James E., Chorba, John S., Lou, Kevin, Dai, Shizhong A., Barrio-Hernandez, Inigo, Memon, Danish, Hernandez-Armenta, Claudia, Perica, Tina, Ganesan, Sai J., Saltzberg, Daniel J., Calviello, Lorenzo, Venkataramanan, Srivats, Lin, Yizhu, Liu, YongFeng, Wankowicz, Stephanie A., Bohn, Markus, Safari, Maliheh, Ugur, Fatima S., Koh, Cassandra, Savar, Nastaran Sadat, Tran, Quang Dinh, Fletcher, Sabrina J., Cai, Yiming, Chang, Jason C. J., Broadhurst, David J., Klippsten, Saker, Sharp, Phillip P., Kuzuoglu-Ozturk, Duygu, Wang, Hao-Yuan, Trenker, Raphael, Cavero, Devin A., Hiatt, Joseph, Roth, Theodore L., Rathore, Ujjwal, Subramanian, Advait, Noack, Julia, Hubert, Mathieu, Stroud, Robert M., Frankel, Alan D., Verba, Kliment A., Agard, David A., Emerman, Michael, Jura, Natalia, von Zastrow, Mark, Verdin, Eric, Ashworth, Alan, Schwartz, Olivier, Mukherjee, Shaeri, Jacobson, Matt, Fujimori, Danica G., Ideker, Trey, Craik, Charles S., Floor, Stephen N., Fraser, James S., Gross, John D., Roth, Bryan L., Ruggero, Davide, Taunton, Jack, Beltrao, Pedro, Vignuzzi, Marco, Shokat, Kevan M., Shoichet, Brian K., Krogan, Nevan J.

“…A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019…”
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A SARS-CoV-2 protein interaction map reveals targets for drug repurposing by Gordon, David E, Jang, Gwendolyn M, Bouhaddou, Mehdi, Xu, Jiewei, Obernier, Kirsten, White, Kris M, O'Meara, Matthew J, Rezelj, Veronica V, Guo, Jeffrey Z, Swaney, Danielle L, Tummino, Tia A, Hüttenhain, Ruth, Kaake, Robyn M, Richards, Alicia L, Tutuncuoglu, Beril, Foussard, Helene, Batra, Jyoti, Haas, Kelsey, Modak, Maya, Kim, Minkyu, Haas, Paige, Polacco, Benjamin J, Braberg, Hannes, Fabius, Jacqueline M, Eckhardt, Manon, Soucheray, Margaret, Bennett, Melanie J, Cakir, Merve, McGregor, Michael J, Li, Qiongyu, Meyer, Bjoern, Roesch, Ferdinand, Vallet, Thomas, Mac Kain, Alice, Miorin, Lisa, Moreno, Elena, Naing, Zun Zar Chi, Zhou, Yuan, Peng, Shiming, Shi, Ying, Zhang, Ziyang, Shen, Wenqi, Kirby, Ilsa T, Melnyk, James E, Chorba, John S, Lou, Kevin, Dai, Shizhong A, Barrio-Hernandez, Inigo, Memon, Danish, Hernandez-Armenta, Claudia, Lyu, Jiankun, Mathy, Christopher J P, Perica, Tina, Pilla, Kala Bharath, Ganesan, Sai J, Saltzberg, Daniel J, Rakesh, Ramachandran, Liu, Xi, Rosenthal, Sara B, Calviello, Lorenzo, Venkataramanan, Srivats, Liboy-Lugo, Jose, Lin, Yizhu, Huang, Xi-Ping, Liu, YongFeng, Wankowicz, Stephanie A, Bohn, Markus, Safari, Maliheh, Ugur, Fatima S, Koh, Cassandra, Savar, Nastaran Sadat, Tran, Quang Dinh, Shengjuler, Djoshkun, Fletcher, Sabrina J, O'Neal, Michael C, Cai, Yiming, Chang, Jason C J, Broadhurst, David J, Klippsten, Saker, Sharp, Phillip P, Wenzell, Nicole A, Kuzuoglu-Ozturk, Duygu, Wang, Hao-Yuan, Trenker, Raphael, Young, Janet M, Cavero, Devin A, Hiatt, Joseph, Roth, Theodore L, Rathore, Ujjwal, Subramanian, Advait, Noack, Julia, Hubert, Mathieu, Stroud, Robert M, Frankel, Alan D, Rosenberg, Oren S, Verba, Kliment A, Agard, David A, Ott, Melanie, Emerman, Michael, Jura, Natalia

“…A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019…”
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Property-Unmatched Decoys in Docking Benchmarks by Stein, Reed M, Yang, Ying, Balius, Trent E, O’Meara, Matt J, Lyu, Jiankun, Young, Jennifer, Tang, Khanh, Shoichet, Brian K, Irwin, John J

“…Enrichment of ligands versus property-matched decoys is widely used to test and optimize docking library screens. However, the unconstrained optimization of…”
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Structures of the [sigma].sub.2 receptor enable docking for bioactive ligand discovery by Alon, Assaf, Lyu, Jiankun, Braz, Joao M, Tummino, Tia A, Craik, Veronica, O'Meara, Matthew J, Webb, Chase M

“…The [sigma].sub.2 receptor has attracted intense interest in cancer imaging.sup.1, psychiatric disease.sup.2, neuropathic pain.sup.3-5 and other areas of…”
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AlphaFold2 structures guide prospective ligand discovery by Lyu, Jiankun, Kapolka, Nicholas, Gumpper, Ryan, Alon, Assaf, Wang, Liang, Jain, Manish K, Barros-Álvarez, Ximena, Sakamoto, Kensuke, Kim, Yoojoong, DiBerto, Jeffrey, Kim, Kuglae, Glenn, Isabella S, Tummino, Tia A, Huang, Sijie, Irwin, John J, Tarkhanova, Olga O, Moroz, Yurii, Skiniotis, Georgios, Kruse, Andrew C, Shoichet, Brian K, Roth, Bryan L

“…AlphaFold2 (AF2) models have had wide impact but mixed success in retrospective ligand recognition. We prospectively docked large libraries against unrefined…”
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Discovery and Rational Design of Pteridin-7(8H)‑one-Based Inhibitors Targeting FMS-like Tyrosine Kinase 3 (FLT3) and Its Mutants by Sun, Deheng, Yang, Yu, Lyu, Jiankun, Zhou, Wei, Song, Wenlin, Zhao, Zhenjiang, Chen, Zhuo, Xu, Yufang, Li, Honglin

“…FLT3 has been validated as a therapeutic target for the treatment of acute myeloid leukemia (AML). In this paper, we describe for the first time,…”
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Discovery of peptide inhibitors targeting human programmed death 1 (PD-1) receptor by Li, Qiao, Quan, Lina, Lyu, Jiankun, He, Zenghui, Wang, Xia, Meng, Jiajia, Zhao, Zhenjiang, Zhu, Lili, Liu, Xiaofeng, Li, Honglin

“…Blocking the interaction of human programmed death 1 (hPD-1) and its ligand hPD-L1 has been a promising immunotherapy in cancer treatment. In this paper, using…”
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Selectivity Challenges in Docking Screens for GPCR Targets and Antitargets by Weiss, Dahlia R, Karpiak, Joel, Huang, Xi-Ping, Sassano, Maria F, Lyu, Jiankun, Roth, Bryan L, Shoichet, Brian K

“…To investigate large library docking’s ability to find molecules with joint activity against on-targets and selectivity versus antitargets, the dopamine D2 and…”
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Active Deep Learning Technique for Underwater Target Recognition by Lyu, Jiankun, Jiang, Longyu, Yang, Chao, Wang, Shijie

“…Underwater target recognition task based on sonar signal data suffers from both professionalism requirement and high time cost during data annotation stages…”
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Large library docking identifies positive allosteric modulators of the calcium-sensing receptor by Liu, Fangyu, Wu, Cheng-Guo, Tu, Chia-Ling, Glenn, Isabella, Meyerowitz, Justin, Kaplan, Anat Levit, Lyu, Jiankun, Cheng, Zhiqiang, Tarkhanova, Olga O, Moroz, Yurii S, Irwin, John J, Chang, Wenhan, Shoichet, Brian K, Skiniotis, Georgios

“…Positive allosteric modulator (PAM) drugs enhance the activation of the calcium-sensing receptor (CaSR) and suppress parathyroid hormone (PTH) secretion…”
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