Dataset Open Access

High quality protein residues: top2018 mainchain-filtered residues

Williams, Christopher; Richardson, David; Richardson, Jane

Introduction
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This directory contains files from the top2018 dataset by the Richardson Lab at Duke University.

These are high-quality residues from high-quality, low redundancy protein chains in the PDB.

This dataset is quality-filtered on mainchain atoms.  For the full-residue filtered set, see https://doi.org/10.5281/zenodo.5115232

The accompanying publication is:
Williams, C. J., Richardson, D. C., & Richardson, J. S. (2021). The importance of residue‐level filtering, and the Top2018 best‐parts dataset of high‐quality protein residues. Protein Science. http://doi.org/10.1002/pro.4239

Usage recommendations
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Protein residues that fail the filtering criteria described below have been removed from the files.  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.  As long as the question concerns mainchain protein atoms, these files should be usable as is.  There is a separate version that has been filtered on all atoms that is suitable for sidechains.

The top2018 contains several different levels of homology clustering (30%, 50%, 70%, 90%) to ensure nonredundant datasets.  The 70% homology level is a reliable default.  These chains are listed in top2018_chains_hom70_mcfilter_60pct_complete.txt and found in top2018_pdbs_mc_filtered_hom70.tar.gz

Files are organized in subdirectories based on the first two letters of their PDB ids.  The included python script sample_file_loop.py may aid in accessing the directory structure.

Files already contain hydrogens added by Reduce.  NQH flips have been performed to ensure that these are the best versions of these structures.

top2018_metadata_mc_filtered.csv contains information on release date, resolution, and validation scores for each file.

top2018_passrates_mc_filtered.csv contains information on how many protein residues from the original chain passed the quality filters.


Homology sets:
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Using sequence homology clusters provided by the RCSB PDB, for each homology cluster, the best chain was selected for inclusion in the dataset.  This ensures minimal sequence/structural redundancy.

The top2018 is available at several different levels of homology clustering, which may be appropriate to different uses.  Lists of the included chains at each homology level are included in this distribution.

Lower homology numbers mean less redundancy, but fewer total chains in the dataset.

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_mcfilter_60pct_complete.txt


Usage caveats:
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These files are incomplete.  They are single chains from structures that may have had multiple chains.  Residues that fail the filtering criteria have been removed.  Programs with strong requirements for completeness or uninterrupted chains should be used with care.  Chain completeness and fragmentation statistics are available in top2018_passrates_mc_filted.csv and in USER records at the end on each .pdb file.

All header information from the original structure has been preserved.  This includes information about chains and residues no longer present in the file.

All ligands and waters associated with the chain have been preserved without filtering.  Robust ligand filtering is beyond the scope of this dataset.  Trust the ligands at your own discretion.

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


Filtering criteria: Chain level
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Chain is protein
Released on or before Dec 31, 2018
Resolution < 2.0
MolProbity Score < 2.0
<3% residues have cbeta deviations
<2% residues have covalent bond length outliers
<2% residues have covalent bond geometry outliers

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.


Filtering criteria: Residue level
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Even excellent structures usually contain some poorly-resolved regions.  Residue-level filtering helps avoid including these regions in otherwise high-quality data

Mainchain atoms are defined as N, CA, C, O, CB.
Note that CB is included, since its ideal position is defined by the other mainchan atoms.

All mainchain atoms in a residue:
Bfactor <= 40
Real-space correlation coefficient (rscc) >= 0.7
2Fo-Fc map value >= 1.2

Additionally, residues are not allowed to have:
Covalent geometry outliers
Steric overlaps or "clashes", as per Probe
Alternate conformations


Chain Completeness criteria
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Chains which lost >40% of their residues during filtering were dropped from this dataset.  All chains present here are at least 60% complete.


Filtering doumentation
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Each file documents its pruned and included residues with USER records.  These include self-documenting USER  DOC lines as follow:
USER  DOC Lines marked with USER  DEL list residues pruned by
USER  DOC quality filtering.
USER  DOC Format is chain:resseq:icode:reason_for_pruning
USER  DOC Reasons for pruning are abbreviated as 1-letter codes: bcmgoa
USER  DOC b=bfactor, c=real space correlation, m=2Fo-Fc mapvalue
USER  DOC g=geometry outlier, o=steric overlap, a=alternate conformations
USER  DOC Lines marked USER  INC list the uninterrupted fragments of structure
USER  DOC still included after pruning by quality filtering
USER  DOC Format is chain1:resseq1:icode1:chain2:resseq2:icode2:fragment_length
USER  DOC where 1 is the first and 2 the last residue of the fragment
USER  DOC Line marked with USER  PCT gives statistics for structure completeness

Version history
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Version 0.9 10.5281/zenodo.4626150     Mar 21, 2021
Initial version

Version 1.0 10.5281/zenodo.5115075     Jul 19, 2021
Split into 30, 50, 70, and 90% homology sets

Version 2.0
Set case of filenames to unambiguous standard: all lowercase except L

Version 2.01

Added missing chain list for recommended hom70 set

Files (4.7 GB)
Name Size
README_mc_filter.txt
md5:750f8826827c5369a1ce46c1117acb54
6.8 kB Download
sample_file_loop.py
md5:f542f9a7ce0f4c220da7ba16c430fc6b
641 Bytes Download
top2018_chains_hom30_mcfilter_60pct_complete.txt
md5:aaa1b4dbc1191489ed6e05cf6060fbb5
58.1 kB Download
top2018_chains_hom50_mcfilter_60pct_complete.txt
md5:8b955c245684bbd76ff23436f79a5445
82.6 kB Download
top2018_chains_hom70_mcfilter_60pct_complete.txt
md5:4e1d77c173f33ec5f2df9aada2901747
95.7 kB Download
top2018_chains_hom90_mcfilter_60pct_complete.txt
md5:72bdb96c209ae36b59dd1b4f71361064
106.3 kB Download
top2018_metadata_mc_filtered.csv
md5:eecc82da39bed07f3d26bdb6d5272c2d
2.0 MB Download
top2018_passrates_mc_filtered.csv
md5:9ad257bd0b521aa0cfc1a986d869060f
340.3 kB Download
top2018_pdbs_mc_filtered_hom30.tar.gz
md5:c80be319fcdc7ca3072a1344af5b7aba
782.1 MB Download
top2018_pdbs_mc_filtered_hom50.tar.gz
md5:7197acde2313b0a1da84786b0e897bd2
1.1 GB Download
top2018_pdbs_mc_filtered_hom70.tar.gz
md5:31ec0d70c296b63891d8e57f8fd546a4
1.3 GB Download
top2018_pdbs_mc_filtered_hom90.tar.gz
md5:fd1671aa7e88e49335ff44e87d96883c
1.5 GB Download
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