FTDMP: A Framework for Protein-Protein, Protein-DNA, and Protein-RNA Docking and Scoring.

IF 3.2 4区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Proteins-Structure Function and Bioinformatics Pub Date : 2025-01-02 DOI:10.1002/prot.26792

Kliment Olechnovič, Rita Banciul, Justas Dapkūnas, Česlovas Venclovas

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引用次数: 0

Abstract

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 the ranking of user-provided 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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FTDMP：蛋白质-蛋白质，蛋白质- dna和蛋白质- rna对接和评分的框架。

FTDMP是一个用于生物分子对接和评分的软件框架。它可以对含有一个或多个蛋白质、DNA或RNA链的亚基进行对接，然后对结果模型进行后续评分。FTDMP还可用于对任何结构预测方法生成的用户提供的生物分子复合物模型进行排序。FTDMP根据基于共识的方法VoroIF-jury评估模型，该方法结合了从生物分子结构的Voronoi细分中获得的个体分数。除了默认的评分模式，FTDMP可以很容易地采用额外的分数；因此，它可以用作评估新开发的评分功能的工具。在最近的CAPRI实验中，FTDMP在盲测中进行了评估，并使用了蛋白质、蛋白质- dna和蛋白质- rna对接基准。它被证明是一个有用的工具，用于不同的研究任务，与建模生物分子相互作用有关。该软件、清理过的对接基准测试和基准测试结果可在https://bioinformatics.lt/software/ftdmp/上获得。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Proteins-Structure Function and Bioinformatics 生物-生化与分子生物学

CiteScore

5.90

自引率

3.40%

发文量

172

审稿时长

3 months

期刊介绍： PROTEINS : Structure, Function, and Bioinformatics publishes original reports of significant experimental and analytic research in all areas of protein research: structure, function, computation, genetics, and design. The journal encourages reports that present new experimental or computational approaches for interpreting and understanding data from biophysical chemistry, structural studies of proteins and macromolecular assemblies, alterations of protein structure and function engineered through techniques of molecular biology and genetics, functional analyses under physiologic conditions, as well as the interactions of proteins with receptors, nucleic acids, or other specific ligands or substrates. Research in protein and peptide biochemistry directed toward synthesizing or characterizing molecules that simulate aspects of the activity of proteins, or that act as inhibitors of protein function, is also within the scope of PROTEINS. In addition to full-length reports, short communications (usually not more than 4 printed pages) and prediction reports are welcome. Reviews are typically by invitation; authors are encouraged to submit proposed topics for consideration.