DOI: 10.5281/zenodo.6859370
title: Polymerase Structure Alignments - v4 Update (July 2022)

description: v4 update (July 2022) of superposed viral polymerase structures using the methodology described in <br> <em>A Comprehensive Superposition of Viral Polymerase Structures</em> by Olve Peersen, Viruses 2019 11(8) 745. • <strong>_All_PDBs_v4.zip</strong> contains a single directory with coordinate files for 917 structures taken from 628 PDB entries. Uncompressed size is 1.6 GB. • <strong>Polymerases_v4.zip</strong> contains the complete set of files from the superpositions, including the _All_PDBs/ directory. Uncompressed size is 5.7 GB. ---------------------------------------------------------------------------------------------------------------<br> POLYMERASE STRUCTURES community page at Zenodo.org v4 Release July 19, 2022 917 structures from 628 PDB entries http://www.zenodo.org/communities/pols/ <br> ========================================================================================= This directory contains a large collection viral polymerase structure coordinates that have been superposed using the methods described in Peersen, Viruses 2019, 11(8), 745. They are released into the public domain under the Creative Commons Attribution (CC BY) license. Please cite the following two references for any derivative work: 1) Reference to the publication describing the methodology:<br> Peersen, OB<br> A Comprehensive Superposition of Viral Polymerase Structures.<br> Viruses 2019, 11(8), 745 <br> https://doi.org/10.3390/v11080745 2) DOI reference that always resolves to the latest release of the dataset:<br> Peersen, OB<br> Polymerase Structure Alignments<br> https://doi.org/10.5281/zenodo.3361874 <br> ---------------------------------------------------------------------------------------------<br> Olve Peersen Olve.Peersen@ColoState.edu<br> Professor<br> Biochemistry & Molecular Biology<br> 1870 Campus Delivery<br> Colorado State University<br> Ft. Collins, CO 80523-1870<br> ------------------------------------------------------------------------- ============================================================================= v4 220719 - Many updates and several news sets, as outlined below. <br> The total count is now 917 polymerase structures from 628 PDB entries 2-rddp: Foamyvirus FOAM added, but rest of set left unchanged 3-dsdn: Simplified as hsv1 was pulled into its own set (see below) <br> NEW alph: Alphaviruses - RRV: 7f0s,<br> SINV: 7vb4, 7vw5 aren: Lassa: 7ckl, 7ela, 7och, 7oe3, 7oe7, 7oea, 7oeb,<br> 7ojj, 7ojk, 70jl, 7ojn<br> Machupo: 7ckm, 7el9, 7elb, 7elc, 7vgq, 7vh1, 7vh2, 7vh3 buny: RVF: 7eei<br> LaCrosse: 7ori, 7orj, 7ork, 7orl, 7orm, 7orn, 7oro coro: 7dfg, 7dfh, 7doi, 7dok, 7dte, 7ed5, 7egq, 7eiz, 7krn, 7kro, 7krp, <br> 7oyg, 7ozu, 7ozv, 7rdx, 7rdy, 7rdz, 7re0, 7re1, 7re2, 7re3, 7thm fluv: 7nha, 7nhc, 7nhx, 7ni0, 7nik, 7nil, 7nir, 7nis, 7nj3, 7nj4, 7nj5, <br> 7nj7, 7nk1, 7nk2, 7nk4, 7nk6, 7nk8, 7nka, 7nkc, 7nki, 7nkr, 7z42, <br> 7z43, 7z43, 7z4o, 7z4o NEW foam: Foamyviruses - 7o0g, 7o0h, 7024<br> Created FOAM.pdb from core of 7o0g.pdb, which was <br> superposed on rddp set, but the orientations of other <br> members of that set (HIV,MMLV,TERT) were not updated. NEW hsv1: Herpes Simplex Virus - 2gv9, 7luf pest: Classic Swine Fever Virus: 7ekj poxv: 7amv, 7aof, 7aoh, 7aoz, 7ap8, 7ap9 rb69: 2atq, 7f4y tavp: 7om2, 7om6, 7om7, 7om9, 7oma<br>
description: Supported by National Institutes of Health (US) grant R01 AI059130 to O.P.
description: {"references": ["Peersen OB, A Comprehensive Superposition of Viral Polymerase Structures, Viruses 2019 11(8) 745."]}