![]() ![]() It includes a fast statistical force field computed from the distances found in the training dataset (resolution smaller than 2.5Å) to quickly evaluate and filter the 3D docking models. PADA1 uses a training set of 2103 high quality DNA-Protein complexes extracted from the Protein Data Bank (PDB). The design of PADA1 relies on protein (pepX) and dsDNA (dnaX) fragments pairs (intX) standing for an interaction. PADA1 (Protein Assisted Dna Assembly version 1) is an extension of the ModelX tool suite developed for the design of dsDPi interactions. PADA1 (PROTEIN ASSISTED DNA ASSEMBLY v1 -> DNA-PROTEIN Docking) Together with the latest (version 5) FoldX protein design tool suite, we were able to engineer backbone- and side chain-compatible interfaces using naked protein structures as input. In this study, areas under the curve of up to 0.86 were achieved on binding site prediction, showing the accuracy and coverage of our approach over established and in-house benchmarking sets. The design of RnaX relies on protein (pepX) and RNA (rnaX) fragments pairs (intX) standing for an interaction. This method has already been successful for designing DNA-protein and protein-protein interfaces. RNA–protein complexes in the Protein Data Bank were decomposed into small peptide-oligonucleotide inter-acting fragment pairs and used as building blocks to assemble big scaffolds representing complex RNA-protein interactions. RnaX is a new extension of the ModelX tool suite developed for the design of Protein–RNA interactions. RNAX (PROTEIN ASSISTED RNA ASSEMBLY -> RNA-PROTEIN Docking) In other words, it is based on usage of fragment libraries as building blocks and developed to predict or reconstruct biomolecules and its interactions. The fragment libraries contain links between spatially close items as they are found in thousands of crystal structures creating in this way a collection of interacting pairs (intX) that are the key for the algorithms to generate docking models and statistical force fields for fast evaluation of the models generated. ModelX modeling toolsuite uses fragment libraries as 3D puzzle pieces in order to recompose interaction conformational spaces. This assumption has been proved to be useful predicting dsDPi (double strand DNA-Protein interactions) and RPi (RNA-Protein interactions) and PPi using naked protein structures (in PDB format) as input. ModelX is a toolsuite for biomolecular modeling inspired on the assumption that Molecular Biology conformational landscape is huge but limited, and also on the fact that interactions between biological entities can be decomposed into small structural motifs that are recycled and reused by nature while shaping new relationships. ModelX: A toolsuite for molecular modeling ![]()
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