Accès ouvert
2026
article
OpenAlex
Trent E. Balius, Marcin D. Dyba, Vandana Kumari, J. L. Denson et autres
Disulfide tethering is a site-directed method of drug discovery used to identify hits for challenging targets. We applied tethering to target oncogenic KRAS, a small GTPase once considered undruggable due to its high nucleotide affinity and a perceived absence of binding sites. …
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2026
conference-abstract
OpenAlex
Matthew J. Whitley, Marcin D. Dyba, Mayukh Chakrabarti, Brian Smith et autres
Abstract Acquired resistance remains a major challenge in the treatment of KRAS-G12C-driven cancers. Secondary mutations in KRAS frequently arise under the selective pressure of KRAS-G12C inhibitors, undermining therapeutic efficacy. These resistance mutations predominantly cluster within or adjacent to the Switch-II pocket, the …
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2026
conference-abstract
OpenAlex
Trent E. Balius, Marcin D. Dyba, Vandana Kumari, John-Paul Denson et autres
Abstract Disulfide tethering is a site-directed method for identifying hits of challenging drug targets. We describe the creation of a screening library of over 2000 disulfide fragments. We have screened 1000+ fragments from this library against 83 engineered KRAS cysteine mutants to …
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Accès ouvert
2025
article
OpenAlex
Yu-Hong Tan, Mayukh Chakrabarti, Reed M. Stein, Lauren E. Prentis et autres
Molecular docking methods are widely used in drug discovery efforts. RAS proteins are important cancer drug targets, and are useful systems for evaluating docking methods, including accounting for solvation effects and covalent small molecule binding. Water often plays a key role in …
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Accès ouvert
2024
preprint
OpenAlex
Yu-Hong Tan, Mayukh Chakrabarti, Reed M. Stein, Lauren E. Prentis et autres
Molecular docking methods are widely used in drug discovery efforts. RAS proteins are important cancer drug targets, and are useful systems for evaluating docking methods, including accounting for solvation effects and covalent small molecule binding. Water often plays a key role in …
us
(code pays fourni par la source)
Accès ouvert
2024
article
OpenAlex
Lorenzo I. Finci, Mayukh Chakrabarti, Gülçin Gülten, Joseph D Finney et autres
RAF kinases are integral to the RAS-MAPK signaling pathway, and proper RAF1 folding relies on its interaction with the chaperone HSP90 and the cochaperone CDC37. Understanding the intricate molecular interactions governing RAF1 folding is crucial for comprehending this process. Here, we present …
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2024
book-chapter
OpenAlex
Mayukh Chakrabarti, Y. Stanley Tan, Trent E. Balius
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Accès ouvert
2023
article
OpenAlex
Trent E. Balius, Yu-Hong Tan, Mayukh Chakrabarti
To allow DOCK 6 access to unprecedented chemical space for screening billions of small molecules, we have implemented features from DOCK 3.7 into DOCK 6, including a search routine that traverses precomputed ligand conformations stored in a hierarchical database. We tested them …
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Accès ouvert
2023
preprint
OpenAlex
Trent E. Balius, Mayukh Chakrabarti, Y. Stanley Tan
To allow DOCK 6 access to unprecedented chemical space for screening billions of small molecules, we have implemented features from DOCK 3.7 into DOCK 6, including a search routine that traverses precomputed ligand conformations stored in a hierarchical database. We tested them …
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Accès ouvert
2021
erratum
OpenAlex
Brian J. Bender, Stefan Gahbauer, Andreas Luttens, Jiankun Lyu et autres
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Accès ouvert
2021
article
OpenAlex
Brian J. Bender, Stefan Gahbauer, Andreas Luttens, Jiankun Lyu et autres
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Accès ouvert
2021
article
OpenAlex
Anna Sophia Kamenik, Isha Singh, Parnian Lak, Trent E. Balius et autres
Significance The dynamic nature of biomolecules is typically neglected in docking screens for ligand discovery. The key to benefitting from various receptor conformations is not only structural but also thermodynamic information. Here, we test a general approach that uses conformational preferences from …
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