Polymerase Structure Alignments - v4 Update (July 2022)

v4 update (July 2022) of superposed viral polymerase structures using the methodology described in 
A Comprehensive Superposition of Viral Polymerase Structures by Olve Peersen, Viruses 2019 11(8) 745.

  •  _All_PDBs_v4.zip contains a single directory with coordinate files for 917 structures taken from 628 PDB entries.  Uncompressed size is 1.6 GB.

  • Polymerases_v4.zip contains the complete set of files from the superpositions, including the _All_PDBs/ directory.   Uncompressed size is 5.7 GB.

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                POLYMERASE STRUCTURES community page at Zenodo.org 

                           v4 Release  July 19, 2022

                        917 structures from 628 PDB entries

                      http://www.zenodo.org/communities/pols/ 
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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:
              Peersen, OB
              A Comprehensive Superposition of Viral Polymerase Structures.
              Viruses 2019, 11(8), 745   
              https://doi.org/10.3390/v11080745

   2) DOI reference that always resolves to the latest release of the dataset:
              Peersen, OB
              Polymerase Structure Alignments
              https://doi.org/10.5281/zenodo.3361874

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Olve Peersen                                Olve.Peersen@ColoState.edu
Professor
Biochemistry & Molecular Biology
1870 Campus Delivery
Colorado State University
Ft. Collins, CO  80523-1870
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v4    220719 - Many updates and several news sets, as outlined below. 
         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)

    NEW    alph: Alphaviruses -      RRV: 7f0s,
                    SINV: 7vb4, 7vw5

        aren:    Lassa:    7ckl, 7ela, 7och, 7oe3, 7oe7, 7oea, 7oeb,
                                   7ojj, 7ojk, 70jl, 7ojn
                   Machupo: 7ckm, 7el9, 7elb, 7elc, 7vgq, 7vh1, 7vh2, 7vh3

        buny:    RVF:   7eei
                     LaCrosse: 7ori, 7orj, 7ork, 7orl, 7orm, 7orn, 7oro

        coro:     7dfg, 7dfh, 7doi, 7dok, 7dte, 7ed5, 7egq, 7eiz, 7krn, 7kro, 7krp, 
                     7oyg, 7ozu, 7ozv, 7rdx, 7rdy, 7rdz, 7re0, 7re1, 7re2, 7re3, 7thm 

        fluv:    7nha, 7nhc, 7nhx, 7ni0, 7nik, 7nil, 7nir, 7nis, 7nj3, 7nj4, 7nj5, 
                   7nj7, 7nk1, 7nk2, 7nk4, 7nk6, 7nk8, 7nka, 7nkc, 7nki, 7nkr, 7z42, 
                   7z43, 7z43, 7z4o, 7z4o

    NEW    foam: Foamyviruses - 7o0g, 7o0h, 7024
                   Created FOAM.pdb from core of 7o0g.pdb, which was 
                   superposed on rddp set, but the orientations of other 
                   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