Dataset Open Access
Williams, Christopher;
Richardson, David;
Richardson, Jane
<?xml version='1.0' encoding='UTF-8'?> <record xmlns="http://www.loc.gov/MARC21/slim"> <leader>00000nmm##2200000uu#4500</leader> <controlfield tag="005">20211213211739.0</controlfield> <controlfield tag="001">4626150</controlfield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Duke University</subfield> <subfield code="0">(orcid)0000-0001-5069-343X</subfield> <subfield code="a">Richardson, David</subfield> </datafield> <datafield tag="700" ind1=" " ind2=" "> <subfield code="u">Duke University</subfield> <subfield code="0">(orcid)0000-0002-3311-2944</subfield> <subfield code="a">Richardson, Jane</subfield> </datafield> <datafield tag="856" ind1="4" ind2=" "> <subfield code="s">3898</subfield> <subfield code="z">md5:43bb05438a213cc392b16c59d9b22d28</subfield> <subfield code="u">https://zenodo.org/record/4626150/files/README</subfield> </datafield> <datafield tag="856" ind1="4" ind2=" "> <subfield code="s">1448266962</subfield> <subfield code="z">md5:b4f5ce0d862a080084b139da9002be6b</subfield> <subfield code="u">https://zenodo.org/record/4626150/files/top2018_mc_filtered_pdbs.tar.gz</subfield> </datafield> <datafield tag="542" ind1=" " ind2=" "> <subfield code="l">open</subfield> </datafield> <datafield tag="260" ind1=" " ind2=" "> <subfield code="c">2021-03-21</subfield> </datafield> <datafield tag="909" ind1="C" ind2="O"> <subfield code="p">openaire_data</subfield> <subfield code="o">oai:zenodo.org:4626150</subfield> </datafield> <datafield tag="100" ind1=" " ind2=" "> <subfield code="u">Duke University</subfield> <subfield code="0">(orcid)0000-0002-5808-8768</subfield> <subfield code="a">Williams, Christopher</subfield> </datafield> <datafield tag="245" ind1=" " ind2=" "> <subfield code="a">High quality protein residues: top2018 mainchain-filtered residues</subfield> </datafield> <datafield tag="540" ind1=" " ind2=" "> <subfield code="u">https://creativecommons.org/licenses/by/4.0/legalcode</subfield> <subfield code="a">Creative Commons Attribution 4.0 International</subfield> </datafield> <datafield tag="650" ind1="1" ind2="7"> <subfield code="a">cc-by</subfield> <subfield code="2">opendefinition.org</subfield> </datafield> <datafield tag="520" ind1=" " ind2=" "> <subfield code="a"><p>Introduction<br> --------------------------------------------------------------------------------<br> This directory contains files from the top2018 dataset by the Richardson Lab at Duke University.</p> <p>These are high-quality residues from high-quality, low redundancy protein chains in the PDB.</p> <p><br> Usage recommendations<br> --------------------------------------------------------------------------------<br> Protein residues that fail the filtering criteria described below have been removed from the files.&nbsp; As a result, these files can be considered pre-filtered and will return only results for residues of good model quality with supporting experimental data.&nbsp; As long as the question concerns mainchain protein atoms, these files should be usable as is.</p> <p>The top2018 contains several different levels of homology clustering to ensure nonredundant datasets.&nbsp; The 70% homology level is a reliable default.&nbsp; These chains are listed in top2018_chains_hom70_60pct_complete.txt</p> <p>Files are organized in subdirectories based on the first two letters of their PDB ids.</p> <p>Files already contain hydrogens added by Reduce.&nbsp; NQH flips have been performed to ensure that these are the best versions of these structures.</p> <p>top2018_metadata_mcfilter.csv contains information on release data, resolution, and validation scores.</p> <p>top2018_passrates_mc_filtered.csv contains information on how many protein residues from the original chain passed the quality filters.</p> <p><br> Homology sets:<br> --------------------------------------------------------------------------------<br> Using sequence homology clusters provided by the RCSB PDB, for each homology cluster, the best chain was selected for inclusion in the dataset.&nbsp; This ensures minimal sequence/structural redundancy.</p> <p>The top2018 is available at several different levels of homology clustering, which may be appropriate to different uses.&nbsp; Lists of the included chains at each homology level are included in this distribution.</p> <p>Lower homology numbers mean greater variety and less redundancy, but also fewer total chains in the dataset.</p> <p>For general use, ***we recommend the 70% homology set*** as a good balance between inclusivity and variety. This list is given in the file top2018_chains_hom70_60pct_complete.txt</p> <p><br> Usage caveats:</p> <p>--------------------------------------------------------------------------------<br> These files are incomplete.&nbsp; They are single chains from structures that may have had multiple chains.&nbsp; Residues that fail the filtering criteria have been removed.&nbsp; Programs with strong requirements for completeness or uninterrupted chains should be used with care.</p> <p>All header information from the original structure has been preserved.&nbsp; This includes information about chains and residues no longer present in the file.</p> <p>All ligands and waters associated with the chain have been preserved without filtering.&nbsp; Robust ligand filtering is beyond the scope of this dataset.&nbsp; Trust the ligands at your own discretion.</p> <p>Sidechain atoms beyond CB have not been considered in the filtering.&nbsp; However, all sidechains have been included for residues that passed the mainchain filters.&nbsp; DO NOT use this set of files for serious questions involving sidechains.&nbsp; See our all-atom filtered dataset instead.</p> <p><br> Filtering criteria: Chain level<br> --------------------------------------------------------------------------------<br> Chain is protein<br> Released on or before Dec 31, 2018<br> Resolution &lt; 2.0<br> MolProbity Score &lt; 2.0<br> &lt;3% residues have cbeta deviations<br> &lt;2% residues have covalent bond length outliers<br> &lt;2% residues have covalent bond geometry outliers</p> <p>Using sequence homology clusters provided by the RCSB PDB, for each homology cluster, the chain with the best (lowest) average of Resolution and MolProbity Score was selected.</p> <p><br> Filtering criteria: Residue level<br> --------------------------------------------------------------------------------<br> Even good structures may contain poorly-resolved regions.&nbsp; Residue-level filtering helps avoid including these regions in otherwise high-quality data</p> <p>Mainchain atoms are defined as N, CA, C, O, CB.<br> Note that CB is included, since its ideal position is defined by the other mainchan atoms.</p> <p>All mainchain atoms in a residue:<br> Bfactor &lt;= 40<br> Real-space correlation coefficient (rscc) &gt;= 0.7<br> 2Fo-Fc map value &gt;= 1.2</p> <p>Additionally, residues are not allowed to have:<br> Covalent geometry outliers<br> Steric overlaps or &quot;clashes&quot;, as per Probe<br> Alternate conformations</p> <p><br> Chain Completeness criteria<br> --------------------------------------------------------------------------------<br> Chains which lost &gt;40% of their residues during filtering were dropped from this dataset.&nbsp; All chains present here are at least 60% complete.</p></subfield> </datafield> <datafield tag="773" ind1=" " ind2=" "> <subfield code="n">doi</subfield> <subfield code="i">isVersionOf</subfield> <subfield code="a">10.5281/zenodo.4626149</subfield> </datafield> <datafield tag="024" ind1=" " ind2=" "> <subfield code="a">10.5281/zenodo.4626150</subfield> <subfield code="2">doi</subfield> </datafield> <datafield tag="980" ind1=" " ind2=" "> <subfield code="a">dataset</subfield> </datafield> </record>
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