De novo prediction of explicit water molecule positions by a novel algorithm within the protein design software MUMBO.

ABSTRACT: By mediating interatomic interactions, water molecules play a major role in protein-protein, protein-DNA and protein-ligand interfaces, significantly affecting affinity and specificity. This notwithstanding, explicit water molecules are usually not considered in protein design software because of high computational costs. To challenge this situation, we analyzed the binding characteristics of 60,000 waters from high resolution crystal structures and used the observed parameters to implement the prediction of water molecules in the protein design and side chain-packing software MUMBO. To reduce the complexity of the problem, we incorporated water molecules through the solvation of rotamer pairs instead of relying on solvated rotamer libraries. Our validation demonstrates the potential of ou

SUBMITTER: Kriegel M 

PROVIDER: S-EPMC10550942 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature