Výsledky vyhledávání - "Ann E. Cleves"

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Autor: Qi, Gao, Ann E, Cleves, Xiao, Wang, Yizhou, Liu, Sean, Bowen, Robert Thomas, Williamson, Ajay N, Jain, Edward, Sherer, Mikhail, Reibarkh

Publikováno v: Journal of natural products. 85(6)

Aureobasidin A (abA) is a natural depsipeptide that inhibits inositol phosphorylceramide (IPC) synthases with significant broad-spectrum antifungal activity. abA is known to have two distinct conformations in solution corresponding to

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::dd0522938b07e27a8d59bf9fbf5ff0bf
https://pubmed.ncbi.nlm.nih.gov/35622967

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XGen: Real-Space Fitting of Complex Ligand Conformational Ensembles to X-ray Electron Density Maps

Autor: Charles A. Lesburg, Alexander C. Brueckner, Qiaolin Deng, Ann E. Cleves, Edward C. Sherer, Mikhail Reibarkh, Ajay N. Jain

Publikováno v: Journal of Medicinal Chemistry. 63:10509-10528

We report a new method for X-ray density ligand fitting and refinement that is suitable for a wide variety of small-molecule ligands, including macrocycles. The approach (called "xGen") augments a force field energy calculation with an electron densi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::de61ef0c116f6c0ccb929b0da9c853df
https://doi.org/10.1021/acs.jmedchem.0c01373

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Structure- and Ligand-Based Virtual Screening on DUD-E+: Performance Dependence on Approximations to the Binding Pocket

Autor: Ajay N. Jain, Ann E. Cleves

Publikováno v: Journal of Chemical Information and Modeling. 60:4296-4310

Using the DUD-E+ benchmark, we explore the impact of using a single protein pocket or ligand for virtual screening compared with using ensembles of alternative pockets, ligands, and sets thereof. For both structure-based and ligand-based approaches,

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::eafce1c8e6793ec62a9ca2629962ac7a
https://doi.org/10.1021/acs.jcim.0c00115

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Complex macrocycle exploration: parallel, heuristic, and constraint-based conformer generation using ForceGen

Autor: Mikhail Reibarkh, Ann E. Cleves, Edward C. Sherer, Ajay N. Jain, Xiao Wang, Qi Gao, Yizhou Liu

Publikováno v: Journal of Computer-Aided Molecular Design
Journal of computer-aided molecular design, vol 33, iss 6

ForceGen is a template-free, non-stochastic approach for 2D to 3D structure generation and conformational elaboration for small molecules, including both non-macrocycles and macrocycles. For conformational search of non-macrocycles, ForceGen is both

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::92c601746a4bf5b88d67305a01862771
https://doi.org/10.1007/s10822-019-00203-1

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Structure- and Ligand-Based Virtual Screening on DUD-E

Autor: Ann E, Cleves, Ajay N, Jain

Publikováno v: Journal of chemical information and modeling. 60(9)

Using the DUD-E

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::ed706031dfce5d25ff46cf461e9248fd
https://pubmed.ncbi.nlm.nih.gov/32271577

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Quantitative surface field analysis: learning causal models to predict ligand binding affinity and pose

Autor: Ann E. Cleves, Ajay N. Jain

Publikováno v: Journal of Computer-Aided Molecular Design
Journal of computer-aided molecular design, vol 32, iss 7

We introduce the QuanSA method for inducing physically meaningful field-based models of ligand binding pockets based on structure-activity data alone. The method is closely related to the QMOD approach, substituting a learned scoring field for a pock

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0726d365e6eefd9eb86d49849d8df148
http://europepmc.org/articles/PMC6096883

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