ArticleMethods in molecular biology (Clifton, N.J.)2022
Computational Design of Peptides with Improved Recognition of the Focal Adhesion Kinase FAT Domain.
Article in Methods in molecular biology (Clifton, N.J.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
We describe a two-stage computational protein design (CPD) methodology for the design of peptides binding to the FAT domain of the protein focal adhesion kinase. The first stage involves high-throughput CPD calculations with the Proteus software. The energies of the folded state are described by a physics-based energy function and of the unfolded peptides by a knowledge-based model that reproduces aminoacid compositions consistent with a helicity scale. The obtained sequences are filtered in terms of the affinity and the stability of the complex. In the second stage, design sequences are further evaluated by all-atom molecular dynamics simulations and binding free energy calculations with a molecular mechanics/implicit solvent free energy function.
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