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Dataset Open Access

High quality protein residues: top2018 mainchain-filtered residues

Williams, Christopher; Richardson, David; Richardson, Jane

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  <identifier identifierType="DOI">10.5281/zenodo.4626150</identifier>
      <creatorName>Williams, Christopher</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="">0000-0002-5808-8768</nameIdentifier>
      <affiliation>Duke University</affiliation>
      <creatorName>Richardson, David</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="">0000-0001-5069-343X</nameIdentifier>
      <affiliation>Duke University</affiliation>
      <creatorName>Richardson, Jane</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="">0000-0002-3311-2944</nameIdentifier>
      <affiliation>Duke University</affiliation>
    <title>High quality protein residues: top2018 mainchain-filtered residues</title>
    <date dateType="Issued">2021-03-21</date>
  <resourceType resourceTypeGeneral="Dataset"/>
    <alternateIdentifier alternateIdentifierType="url"></alternateIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.4626149</relatedIdentifier>
    <rights rightsURI="">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
    <description descriptionType="Abstract">&lt;p&gt;Introduction&lt;br&gt;
This directory contains files from the top2018 dataset by the Richardson Lab at Duke University.&lt;/p&gt;

&lt;p&gt;These are high-quality residues from high-quality, low redundancy protein chains in the PDB.&lt;/p&gt;

Usage recommendations&lt;br&gt;
Protein residues that fail the filtering criteria described below have been removed from the files.&amp;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.&amp;nbsp; As long as the question concerns mainchain protein atoms, these files should be usable as is.&lt;/p&gt;

&lt;p&gt;The top2018 contains several different levels of homology clustering to ensure nonredundant datasets.&amp;nbsp; The 70% homology level is a reliable default.&amp;nbsp; These chains are listed in top2018_chains_hom70_60pct_complete.txt&lt;/p&gt;

&lt;p&gt;Files are organized in subdirectories based on the first two letters of their PDB ids.&lt;/p&gt;

&lt;p&gt;Files already contain hydrogens added by Reduce.&amp;nbsp; NQH flips have been performed to ensure that these are the best versions of these structures.&lt;/p&gt;

&lt;p&gt;top2018_metadata_mcfilter.csv contains information on release data, resolution, and validation scores.&lt;/p&gt;

&lt;p&gt;top2018_passrates_mc_filtered.csv contains information on how many protein residues from the original chain passed the quality filters.&lt;/p&gt;

Homology sets:&lt;br&gt;
Using sequence homology clusters provided by the RCSB PDB, for each homology cluster, the best chain was selected for inclusion in the dataset.&amp;nbsp; This ensures minimal sequence/structural redundancy.&lt;/p&gt;

&lt;p&gt;The top2018 is available at several different levels of homology clustering, which may be appropriate to different uses.&amp;nbsp; Lists of the included chains at each homology level are included in this distribution.&lt;/p&gt;

&lt;p&gt;Lower homology numbers mean greater variety and less redundancy, but also fewer total chains in the dataset.&lt;/p&gt;

&lt;p&gt;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&lt;/p&gt;

Usage caveats:&lt;/p&gt;

These files are incomplete.&amp;nbsp; They are single chains from structures that may have had multiple chains.&amp;nbsp; Residues that fail the filtering criteria have been removed.&amp;nbsp; Programs with strong requirements for completeness or uninterrupted chains should be used with care.&lt;/p&gt;

&lt;p&gt;All header information from the original structure has been preserved.&amp;nbsp; This includes information about chains and residues no longer present in the file.&lt;/p&gt;

&lt;p&gt;All ligands and waters associated with the chain have been preserved without filtering.&amp;nbsp; Robust ligand filtering is beyond the scope of this dataset.&amp;nbsp; Trust the ligands at your own discretion.&lt;/p&gt;

&lt;p&gt;Sidechain atoms beyond CB have not been considered in the filtering.&amp;nbsp; However, all sidechains have been included for residues that passed the mainchain filters.&amp;nbsp; DO NOT use this set of files for serious questions involving sidechains.&amp;nbsp; See our all-atom filtered dataset instead.&lt;/p&gt;

Filtering criteria: Chain level&lt;br&gt;
Chain is protein&lt;br&gt;
Released on or before Dec 31, 2018&lt;br&gt;
Resolution &amp;lt; 2.0&lt;br&gt;
MolProbity Score &amp;lt; 2.0&lt;br&gt;
&amp;lt;3% residues have cbeta deviations&lt;br&gt;
&amp;lt;2% residues have covalent bond length outliers&lt;br&gt;
&amp;lt;2% residues have covalent bond geometry outliers&lt;/p&gt;

&lt;p&gt;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.&lt;/p&gt;

Filtering criteria: Residue level&lt;br&gt;
Even good structures may contain poorly-resolved regions.&amp;nbsp; Residue-level filtering helps avoid including these regions in otherwise high-quality data&lt;/p&gt;

&lt;p&gt;Mainchain atoms are defined as N, CA, C, O, CB.&lt;br&gt;
Note that CB is included, since its ideal position is defined by the other mainchan atoms.&lt;/p&gt;

&lt;p&gt;All mainchain atoms in a residue:&lt;br&gt;
Bfactor &amp;lt;= 40&lt;br&gt;
Real-space correlation coefficient (rscc) &amp;gt;= 0.7&lt;br&gt;
2Fo-Fc map value &amp;gt;= 1.2&lt;/p&gt;

&lt;p&gt;Additionally, residues are not allowed to have:&lt;br&gt;
Covalent geometry outliers&lt;br&gt;
Steric overlaps or &amp;quot;clashes&amp;quot;, as per Probe&lt;br&gt;
Alternate conformations&lt;/p&gt;

Chain Completeness criteria&lt;br&gt;
Chains which lost &amp;gt;40% of their residues during filtering were dropped from this dataset.&amp;nbsp; All chains present here are at least 60% complete.&lt;/p&gt;</description>
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