PocketOptimizer 2.0: A modular framework for computer-aided ligand-binding design.

ABSTRACT: The ability to design customized proteins to perform specific tasks is of great interest. We are particularly interested in the design of sensitive and specific small molecule ligand-binding proteins for biotechnological or biomedical applications. Computational methods can narrow down the immense combinatorial space to find the best solution and thus provide starting points for experimental procedures. However, success rates strongly depend on accurate modeling and energetic evaluation. Not only intra- but also intermolecular interactions have to be considered. To address this problem, we developed PocketOptimizer, a modular computational protein design pipeline, that predicts mutations in the binding pockets of proteins to increase affinity for a specific ligand. Its modularity enables u

SUBMITTER: Noske J 

PROVIDER: S-EPMC9793973 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature