Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction | Zendy

Surjit B. Dixit | Zendy; David L. Beveridge | Zendy

Open Access

Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction

Author(s) -

Surjit B. Dixit,

David L. Beveridge

Publication year - 2006

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btl059

Subject(s) - computer science , context (archaeology) , set (abstract data type) , molecular dynamics , interface (matter) , sequence (biology) , data mining , dna , database , bioinformatics , information retrieval , computational biology , chemistry , programming language , genetics , biology , computational chemistry , paleontology , bubble , maximum bubble pressure method , parallel computing

We report here the release of a web-based tool (MDDNA) to study and model the fine structural details of DNA on the basis of data extracted from a set of molecular dynamics (MD) trajectories of DNA sequences involving all the unique tetranucleotides. The dynamic web interface can be employed to analyze the first neighbor sequence context effects on the 10 unique dinucleotide steps of DNA. Functionality is included to build all atom models of any user-defined sequence based on the MD results. The backend of this interface is a relational database storing the conformational details of DNA obtained in 39 different MD simulation trajectories comprising all the 136 unique tetranucleotide steps. Examples of the use of this data to predict DNA structures are included.

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