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Article

Exploration of Cryptic Pockets Using Enhanced Sampling Along Normal Modes: A Case Study of KRAS G12D.

Journal of chemical information and modeling - 11 Nov 2024

Vithani Neha, Zhang She, Thompson Jeffrey P, Patel Lara A, Demidov Alex, Xia Junchao, Balaeff Alexander, Mentes Ahmet, Arnautova Yelena A, Kohlmann Anna, Lawson J David, Nicholls Anthony, Skillman A Geoffrey, LeBard David N

Abstract excerpt

Identification of cryptic pockets has the potential to open new therapeutic opportunities by discovering ligand binding sites that remain hidden in static apo structures of a target protein. Moreover, allosteric cryptic pockets can become valuable for designing target-selective ligands when the natural ligand binding sites are conserved in variants of a protein. For example, before an allosteric cryptic pocket...

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Methodology Data sources Editorial policy Privacy About Contact Helena Bioinformatics

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PMID: 39419500
DOI: 10.1021/acs.jcim.4c01435
PMCID: PMC11558672

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