Article Dans Une Revue Proteins - Structure, Function and Bioinformatics Année : 2025

FTDMP: a framework for protein-protein, protein-DNA and protein-RNA docking and scoring

Résumé

FTDMP is a software framework for biomolecular docking and scoring. It can perform docking of subunits containing one or more protein, DNA or RNA chains, followed by subsequent scoring of the resulting models. FTDMP can also be used for ranking of userprovided models of biomolecular complexes, generated by any structure prediction method.

FTDMP evaluates models according to the consensus-based method VoroIF-jury, which combines individual scores derived from the Voronoi tessellation of biomolecular structures.

In addition to the default scoring mode, FTDMP can easily adopt additional scores, thus it may be used as a tool to assess newly developed scoring functions. FTDMP was evaluated during blind testing in recent CAPRI experiments and using protein-protein, protein-DNA and protein-RNA docking benchmarks. It proved to be a useful tool for different research tasks, related to modeling biomolecular interactions. The software, cleaned docking benchmarks and benchmarking results are available at https://bioinformatics.lt/software/ftdmp/.
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hal-04879411 , version 1 (10-01-2025)

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Kliment Olechnovič, Rita Banciul, Justas Dapkūnas, Česlovas Venclovas. FTDMP: a framework for protein-protein, protein-DNA and protein-RNA docking and scoring. Proteins - Structure, Function and Bioinformatics, In press, ⟨10.1002/prot.26792⟩. ⟨hal-04879411⟩
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