text: user274: Accuracies of protein structure predictors have improved quite a lot in recent years. Algorithms such as Rosetta have gotten robust enough to predict structures of large number of proteins. However, I could't find any initiative to make a database for proteome-wide predictions of protein structures or may be integrate the predicted structures in existing databases (PDB or Uniprot).
  If any such exists, please let me know.
  
  user5180: I am using DMPfold to predict protein structure of a 382 residue protein sequence. All goes wel, and even the files are produced but during the "seq2maps.csh", I get this error in between:
  Running PSIPRED & SOLVPRED
  Running PSI-BLAST with sequence c600m2-tail-before-lysin-sequence.temp.fasta ...
  Segmentation fault (core dumped)
  [blastpgp] WARNING: Unable to open BLOSUM62
  [blastpgp] WARNING: BlastScoreBlkMatFill returned non-zero status
  [blastpgp] WARNING: SetUpBlastSearch failed.
  BLASTP 2.2.17 [Aug-26-2007]
  
  
  Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
  Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
  "Gapped BLAST and PSI-BLAST: a new generation of protein database search
  programs",  Nucleic Acids Res. 25:3389-3402.
  
  
  Reference for composition-based statistics:
  Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,
  Sergei Shavirin, John L. Spouge, Yuri I. Wolf,  
  Eugene V. Koonin, and Stephen F. Altschul (2001), 
  "Improving the accuracy of PSI-BLAST protein database searches with 
  composition-based statistics and other refinements",  Nucleic Acids Res. 29:2994-3005.
  
  Query= C600M2_00100 tail protein [Salmonella phage BPS17S6]
           (377 letters)
  
  Database: c600m2-tail-before-lysin-sequence.a3m 
             46,978 sequences; 11,323,713 total letters
  
  SearchingFATAL: Error whilst running blastpgp - script terminated!
  Running PSICOV
  Running FreeContact
  Running CCMpred
   _____ _____ _____               _ 
  |     |     |     |___ ___ ___ _| |
  |   --|   --| | | | . |  _| -_| . |
  |_____|_____|_|_|_|  _|_| |___|___|
                    |_|              
  
  using CPU (10 thread(s))
  
  Reweighted 30404 sequences with threshold 0.8 to Beff=22917.9 weight mean=0.753779, min=0.0232558, max=1
  
  Will optimize 62686429 32-bit variables
  
  iter    eval    f(x)        ║x║         ║g║         step
  1       1       1.50338e+07 152357      3.021629e+11    1.55e-06
  2       1       1.47369e+07 152356      2.1447226e+11   1.18e-06
  3       1       1.44292e+07 152355      1.4646483e+11   1.22e-06
  4       1       1.41268e+07 152353      1.0388224e+11   1.5e-06
  5       1       1.38295e+07 152358      7.337667e+10    1.92e-06
  
  Can you please let me know if I need to rerun seq2maps.csh because of this error? And, how this error can be solved? Thank you!
  
  user6322: Updated
  As of 2021, the EBI alphaFold2 is the best resource. There are some caveats, which I have outlined in this blog post.
  But majorly, it contains only monomeric predictions and not oligomers and complexes. As a result, for protein with a close homologue with a solved structure, it may be more handy to use a threaded structure as found in the SwissModel database (see original answer below) because it may be oligomeric and/or one can copy over ligands or binding partners if deemed suitable.
  One can make one's own predictions with AlphaFold2, who have released a handy notebook. Also one can make complexes and oligomers with some tweaks or with the heavily improved notebooks found in ColabFold GitHub repo.
  Original Answer
  It is worth saying that for model organisms, Expasy Swissmodel is the "classical" database of predicted proteome structures. It has several model organisms and gets updates regularly. The models are threaded only and the algorithm fell behind some time ago —their website however is modern and sleek. If using Rosetta afterwards, one should do a few cycles of FastRelax with a movemap preventing backbone movements or CA restrained, followed by a couple of cartesian bond/angle fixing cycles: the structure tends to blow up if energy minimised otherwise.
  However, if one had a specific protein in mind predicting with RosettaCM, the I-Tasser server or Phyre server is by the recommended option. And actually, the Phyre server has a dataset of the precomputed human proteome.
  About the PDB, the database has been purged of all in silico models and contains only empirical structures (NMR, X-ray, neutron diffraction and cryo-EM).
  
  user4622: There are three initiatives I know of to have a go at this:
  
  PConsFam, which collects data from this paper.
  The Baker group's metagenomic study which you mention in the question.
  The recent DMPfold work from our lab. This compares its results to the above two studies and discusses the effect on various model organisms.
  
  The second and third of these don't provide a database per se, but the models are available for download and are linked to the Pfam database.
  EDIT: things have moved on significantly since I first wrote this answer. As other answers mention, the AlphaFold Protein Structure Database is now the best resource in this area.
  
  user14009: By far the most accurate model right now should be AlphaFold, and there are open structures across several proteomes available at https://alphafold.ebi.ac.uk/.
  
original_text: 274: <p>Accuracies of protein structure predictors have improved quite a lot in recent years. Algorithms such as <a href="https://www.rosettacommons.org/software" rel="nofollow noreferrer">Rosetta</a> have gotten robust enough to <a href="http://science.sciencemag.org/content/355/6322/294" rel="nofollow noreferrer">predict structures of large number of proteins</a>. However, I could't find any initiative to make a database for proteome-wide predictions of protein structures or may be integrate the predicted structures in existing databases (PDB or Uniprot).</p>
  
  <p>If any such exists, please let me know.</p>
   5180: <p>I am using DMPfold to predict protein structure of a 382 residue protein sequence. All goes wel, and even the files are produced but during the "seq2maps.csh", I get this error in between:</p>
  
  <pre><code>Running PSIPRED &amp; SOLVPRED
  Running PSI-BLAST with sequence c600m2-tail-before-lysin-sequence.temp.fasta ...
  Segmentation fault (core dumped)
  [blastpgp] WARNING: Unable to open BLOSUM62
  [blastpgp] WARNING: BlastScoreBlkMatFill returned non-zero status
  [blastpgp] WARNING: SetUpBlastSearch failed.
  BLASTP 2.2.17 [Aug-26-2007]
  
  
  Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
  Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
  "Gapped BLAST and PSI-BLAST: a new generation of protein database search
  programs",  Nucleic Acids Res. 25:3389-3402.
  
  
  Reference for composition-based statistics:
  Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,
  Sergei Shavirin, John L. Spouge, Yuri I. Wolf,  
  Eugene V. Koonin, and Stephen F. Altschul (2001), 
  "Improving the accuracy of PSI-BLAST protein database searches with 
  composition-based statistics and other refinements",  Nucleic Acids Res. 29:2994-3005.
  
  Query= C600M2_00100 tail protein [Salmonella phage BPS17S6]
           (377 letters)
  
  Database: c600m2-tail-before-lysin-sequence.a3m 
             46,978 sequences; 11,323,713 total letters
  
  SearchingFATAL: Error whilst running blastpgp - script terminated!
  Running PSICOV
  Running FreeContact
  Running CCMpred
   _____ _____ _____               _ 
  |     |     |     |___ ___ ___ _| |
  |   --|   --| | | | . |  _| -_| . |
  |_____|_____|_|_|_|  _|_| |___|___|
                    |_|              
  
  using CPU (10 thread(s))
  
  Reweighted 30404 sequences with threshold 0.8 to Beff=22917.9 weight mean=0.753779, min=0.0232558, max=1
  
  Will optimize 62686429 32-bit variables
  
  iter    eval    f(x)        ║x║         ║g║         step
  1       1       1.50338e+07 152357      3.021629e+11    1.55e-06
  2       1       1.47369e+07 152356      2.1447226e+11   1.18e-06
  3       1       1.44292e+07 152355      1.4646483e+11   1.22e-06
  4       1       1.41268e+07 152353      1.0388224e+11   1.5e-06
  5       1       1.38295e+07 152358      7.337667e+10    1.92e-06
  </code></pre>
  
  <p>Can you please let me know if I need to rerun seq2maps.csh because of this error? And, how this error can be solved? Thank you!</p>
   6322: <h2>Updated</h2>
  <p>As of 2021, the <a href="https://alphafold.ebi.ac.uk/" rel="nofollow noreferrer">EBI alphaFold2</a> is the best resource. There are some caveats, which I have outlined in <a href="https://blog.matteoferla.com/2021/07/what-to-look-out-for-with-alphafold2.html" rel="nofollow noreferrer">this blog post</a>.</p>
  <p>But majorly, it contains only monomeric predictions and not oligomers and complexes. As a result, for protein with a close homologue with a solved structure, it may be more handy to use a threaded structure as found in the SwissModel database (see original answer below) because it may be oligomeric and/or one can copy over ligands or binding partners if deemed suitable.</p>
  <p>One can make one's own predictions with AlphaFold2, who have released a handy notebook. Also one can make complexes and oligomers with some tweaks or with the heavily improved notebooks found in <a href="http://ColabFold%20GitHub%20repo" rel="nofollow noreferrer">ColabFold GitHub repo</a>.</p>
  <h2>Original Answer</h2>
  <p>It is worth saying that for model organisms, Expasy <a href="https://swissmodel.expasy.org/" rel="nofollow noreferrer">Swissmodel</a> is the &quot;classical&quot; database of predicted proteome structures. It has several model organisms and gets updates regularly. The models are threaded only and the algorithm fell behind some time ago —their website however is modern and sleek. If using Rosetta afterwards, one should do a few cycles of FastRelax with a movemap preventing backbone movements or CA restrained, followed by a couple of cartesian bond/angle fixing cycles: the structure tends to blow up if energy minimised otherwise.</p>
  <p>However, if one had a specific protein in mind predicting with RosettaCM, the I-Tasser server or Phyre server is by the recommended option. And actually, the Phyre server has a <a href="http://www.sbg.bio.ic.ac.uk/%7Emissense3d/dataset.html" rel="nofollow noreferrer">dataset of the precomputed human proteome</a>.</p>
  <p>About the PDB, the database has been purged of all <em>in</em> <em>silico</em> models and contains only empirical structures (NMR, X-ray, neutron diffraction and cryo-EM).</p>
   4622: <p>There are three initiatives I know of to have a go at this:</p>
  <ol>
  <li><a href="http://pconsfam.bioinfo.se/" rel="nofollow noreferrer">PConsFam</a>, which collects data from <a href="https://academic.oup.com/bioinformatics/article/33/14/i23/3953955" rel="nofollow noreferrer">this paper</a>.</li>
  <li>The Baker group's <a href="https://science.sciencemag.org/content/355/6322/294" rel="nofollow noreferrer">metagenomic study</a> which you mention in the question.</li>
  <li>The recent <a href="https://arxiv.org/abs/1811.12355" rel="nofollow noreferrer">DMPfold</a> work from our lab. This compares its results to the above two studies and discusses the effect on various model organisms.</li>
  </ol>
  <p>The second and third of these don't provide a database per se, but the models are available for download and are linked to the Pfam database.</p>
  <p>EDIT: things have moved on significantly since I first wrote this answer. As other answers mention, the <a href="https://alphafold.ebi.ac.uk" rel="nofollow noreferrer">AlphaFold Protein Structure Database</a> is now the best resource in this area.</p>
   14009: <p>By far the most accurate model right now should be AlphaFold, and there are open structures across several proteomes available at <a href="https://alphafold.ebi.ac.uk/" rel="nofollow noreferrer">https://alphafold.ebi.ac.uk/</a>.</p>
  