DNATCO: assignment of DNA conformers at dnatco.org

W284–W287 Nucleic Acids Research, 2016, Vol. 44, Web Server issue doi: 10.1093/nar/gkw381 Published online 5 May 2016 DNATCO: assignment of DNA conformers at dnatco.org Jiřı́ Černý, Paulı́na Božı́ková and Bohdan Schneider* Institute of Biotechnology CAS, BIOCEV, Průmyslová 595, 252 50 Vestec, Prague West, Czech Republic Received February 8, 2016; Revised April 25, 2016; Accepted April 26, 2016 ABSTRACT INTRODUCTION The complexity and variability of DNA structures can no more be understood within the traditional ‘A–B–Z structural code’. DNA molecules are able to form sharp kinks in complexes with some transcription factors, spiral around the histone core proteins, accommodate sharp kinks in Holliday junctions, extend their backbone in intercalation complexes with aromatic drugs, or form stable quadruplex or hairpin structures. Surprisingly though, tools allowing to go beyond a simplified picture of DNA structure and reducing its complexity to a few qualitative descriptors are scarce. NDB (1) provides a comprehensive overview of the available structures and offers their limited structure classification, software tool 3DNA (2), concentrating on description of the geometry of base pairing. Several years ago, some of us attempted to classify the geometry of the DNA backbone at the level of dinucleotides (3) and later on, we developed a robust automated pipeline to perform such an analysis (4). In this contribution, we present an improvement of this methodology implemented into a web-based tool that offers an objective analysis of the DNA local conformation based on a rigorous geometrybased algorithm. Conformations of dinucleotide steps are * To MATERIALS AND METHODS Conformations of dinucleotide steps (nomenclature defined in Figure 1) are analyzed by comparing their torsion angles to the torsions of 4439 dinucleotides in the so called ‘golden set’. The golden set is an ensemble of dinucleotides manually curated and classified into one of the 57 conformational classes called ntC. The geometry of the ntC classes is summarized in Supplementary Table S1 and is also available at the dnatco.org website. The assignment begins by uploading a PDB-formatted structure to the website and is performed in the torsional space by comparing values of nine DNA backbone torsion angles of the analyzed step and all 4439 steps in the golden set by the modified k-nearest neighbors algorithm according to the protocol by Čech et al. (4) with modifications. The currently used ntC definitions originate from the set reported by Svozil et al. (3), who described them in detail along with the methods how they were identified. THE DNATCO SERVER Hardware and software The previous version of the DNATCO server (available at dnatco.org/v1) was migrated from a home based hardware and is now hosted as a Linux based virtual machine in the environment provided by the ELIXIR CZ infrastructure. This ensures 24/7 availability and professional maintenance as well as easy scaling of the resources if necessary. The presented second version of the server ran about a year internally and had been tested over a year as a publicly available service accessible at the dnatco.org address. whom correspondence should be addressed. Tel: +420 325 873 766; Email:  C The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact The web service DNATCO (dnatco.org) classifies local conformations of DNA molecules beyond their traditional sorting to A, B and Z DNA forms. DNATCO provides an interface to robust algorithms assigning conformation classes called ntC to dinucleotides extracted from DNA-containing structures uploaded in PDB format version 3.1 or above. The assigned dinucleotide ntC classes are further grouped into DNA structural alphabet ntA, to the best of our knowledge the first DNA structural alphabet. The results are presented at two levels: in the form of user friendly visualization and analysis of the assignment, and in the form of a downloadable, more detailed table for further analysis offline. The website is free and open to all users and there is no login requirement. assigned to one of 57 conformers called ntC. To help interpret the results and the overall structural features of the analyzed structure, the assignment is also interpreted in terms of conceptually simpler structural alphabet ntA consisting of just 12 members, which were created by grouping structurally related ntC. The relatively high number of ntC classes, 57, resulted from the analysis of the available DNA structures and reflects the complexity of the DNA conformational space. In contrast, the particular way of grouping of ntC into letters of the ntA structural alphabet and the number of ntA letters are subjective. Nucleic Acids Research, 2016, Vol. 44, Web Server issue W285 The software part employs Apache web server and PHP5 for the server side scripting. The internal processing of uploaded PDB-formatted structures is performed using the VMD program (5) extracting only nucleic acid atoms for further analysis. The torsion angle measurement and the assignment of ntC conformers itself is performed by in house programs written in the Python programming language. The interactive display of analyzed 3D structures relies on JSmol (6), a JavaScript based molecular viewer running in a browser. The JavaScript allows straightforward transfer of the DNATCO web service to various platforms and devices including mobile devices without a need to install additional applets. The JSmol performance is known to depend on the browser version and the computer operation system used. The complete web service was successfully tested in the major web browser programs under Linux, OS X and Windows with Firefox having currently the best performance in the JSmol part. The home page The home page (snapshot in Supplementary Figure S1 and Table S1) briefly introduces the purpose of the web, defines the dinucleotide step, lists the geometries of the ntC conformers with their brief characterization and provides the tool to upload the structure to be analyzed. The top of the home page contains links to the tutorial section that describes the submission process step by step, explains the results, and also contains the link to a test run using the Dickerson-Drew dodecamer of PDB ID 1bna (7). The PDB formatted structure file can be uploaded either from user’s disk or by typing a PDB four-letter code and pressing the respective SUBMIT button; the former way is useful for structures generated or modified by the user, the latter for analysis of the released PDB structures. Names and brief annotations of the 57 ntC DN (...truncated)