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Documentation

  • Description
  • Funding
  • Resources
  • References
  • Glossary and Software References and Credits
  • Data Formats
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    • DESCRIPTION

    FUNDING

    RESOURCES

    REFERENCES

    GLOSSARY AND SOFTWARE REFERENCES AND CREDITS

      3D-JURY
      Note: 3D-JURY search disabled (2006-12-18)

      Robetta uses a variant of 3D-Jury-A1, a consensus fold recognition method that uses 8 servers: ORFeus, FFAS03, mGenTHREADER, 3D-PSSM, INUB, FUGUE2, and BASIC (dist). A consensus is derived from a single model per server. The procedure selects models only from the servers used for consensus building. 3D-JURY is run remotely on the server provided by Leszek Rychlewski. Putative parent PDBs (but not their alignments) that are detected by this 3D-Jury-A1 variant with sufficient confidence are used as starting points for modeling with Robetta's Comparative Modeling protocol. If your model is based on a 3D-Jury detection, it is recommended to cite the 3D-Jury method as well as the servers listed above on which it depends.

      • Ginalski K, Elofsson A, Fischer D, Rychlewski L. (2003) 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics. 19(8):1015-8.

      3D-Pair
      3D-Pair is a structure-structure alignment program that is used by Robetta in generating StrAD-Stack multiple structural alignments.

      • Plewczynski D, Pas J, von Grotthuss M, Rychlewski L. (2002) 3D-Hit: fast structural comparison of proteins. Appl. Bioinformatics 1(4):223-5

      Condor
      Condor is used to run jobs on the hardware. This product includes software from the Condor Project (http://www.condorproject.org/)

      Coiled-coil Regions
      COILS is used to identify coiled-coil regions.

      • Lupas, A., Van Dyke, M., and Stock, J. (1991) Predicting Coled Coils from Protein Sequences, Science 252:1162-1164.

      Disordered Regions
      DISOPRED is used to identify disordered regions.

      • Jones, D.T. & Ward, J.J. (2003) Prediction of Disordered Regions in Proteins from Position Specific Score Matrices. Proteins, 53 Suppl 6, 573-578.

      Domain Repeats
      REPRO is used to identify distant sequence repeats within a single query sequence likely to represent domain repeats.

      • George RA. and Heringa J. (2000) The REPRO server: finding protein internal sequence repeats through the web. Trends Biochem. Sci. 25, 515-517.

      DSSP
      DSSP defines secondary structure given atomic coordinates.

      • Kabsch,W. and Sander,C. (1983) Biopolymers 22, 2577-2637.

      Exclude Homologues
      Excludes fragments from homologues for the purpose of testing on non-blind targets.

      FFAS03
      Note: FFAS03 search disabled (2006-12-18)

      FFAS03 is a fast remote fold-recognition method that uses residue substitution profile-profile comparison. FFAS03 is run remotely using the server provided by Adam Godzik. Putative parent PDBs (but not their alignments) that are detected by FFAS03 with sufficient confidence are used as starting points for modeling with Robetta's Comparative Modeling protocol. If your model is based on an FFAS03 detection, it is recommended that you cite the FFAS03 server.

      • Jaroszewski L, Rychlewski L, Li Z, Li W, Godzik A. (2005). FFAS03: a server for profile--profile sequence alignments. Nucleic Acids Res. 33(Web Server issue):W284-8.
      • Rychlewski L, Jaroszewski L, Li W, Godzik A. (2000). Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Science 9:232-41
      • Jaroszewski L, Rychlewski L, Godzik A. (2000). Improving the quality of twilight-zone alignments. Protein Science 9:1487-96

      HHSEARCH
      Note: HHSEARCH is now used for remote template detection and is run locally (2008-05-05)

      HHSEARCH is a profile HMM based homology detection and alignment method. Putative parent PDBs (but not their alignments) that are detected by HHSEARCH with sufficient confidence are used as starting points for modeling with Robetta's Comparative Modeling protocol.

      HMM-PFAM
      Pfam is a set of families of protein sequences that are represented as hidden Markov models, and may be searched with HMMER.

      • Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL (2002). The Pfam protein families database. Nucleic Acids Res. 30(1):276-280
      • Eddy, SR (1998) Profile hidden Markov models. Bioinformatics 14:755-63

        HMMER is governed by the GNU Public License

      Identifier
      An optional four or five character alphanumeric identifier like a PDB ID.

      Jufo
      Jufo is a protein secondary structure prediction method that uses primary sequence only.

      • Meiler J, Mueller M, Zeidler A, Schmaeschke F. (2002) JUFO: Secondary Structure Prediction for Proteins, http://www.jens-meiler.de/

      Jufo3D
      Jufo3D is a protein secondary structure prediction method that uses primary sequence and one or more three dimensional models.

      • Meiler J. (2003) JUFO3D: Secondary Structure Prediction for Proteins from low Resolution Tertiary Structure. http://www.jens-meiler.de/

      K*Sync
      K*Sync is a method for aligning a protein sequence onto the sequence/structure of a homolog with an experimentally determined structure for the purpose of homology modeling. The method was developed by Dylan Chivian and David Baker for use in Robetta's Comparative Modeling.

      • Chivian D and Baker D. (2006) Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection. Nucleic Acids Res. 34(17):e112

      Low Complexity
      SEG is used to identify regions of low complexity.

      • Wootton JC, Federhen S. (1996) Analysis of compositionally biased regions in sequence databases. Methods Enzymol. 266:554-71.
      • Wootton JC, Federhen S. (1993) Statistics of local complexity in amino acid sequences and sequence databases. Comput. Chem. 17:149-63.

      MAMMOTH
      MAMMOTH is used to detect structural similarities between de novo models and expermentally determined structures from the PDB. Significant matches (mammoth z-score >= 4.5) are listed on domain result pages. Rasmol scripts of the structural alignments can be downloaded by clicking on the z-scores. Once downloaded, the structural alignments can be viewed with rasmol using the following command 'rasmol -script robetta.MammothRasmol.' For more information about Mammoth, please refer to the following publication:

      • Ortiz AR, Strauss CE, Olmea O. (2002) MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison. Protein Sci. 11:2606-21

      Notes
      Optional text to describe your target.

      Parent
      PDB structure (PDB ID) to use for comparative modeling. Only applies to the structure server for 3-D models. The PDB ID must include the Chain ID or '_' (5 characters are required).

      Parent Range
      Residue number range of the parent to consider. Use sequence numbering for the full parent chain sequence (not the numbering from the coordinates in the parent PDB). Only applies to the structure server for 3-D models.

      Partner Definitions
      For computational alanine scanning. All relevant chains of the       protein complex, and the parter in the complex to which they belong.

      PDB
      Protein Data Bank is the world's protein structure data repository. We also refer to the file format from the Protein Data Bank used to describe a protein structure as a PDB.

      Pfam
      Pfam is a set of families of protein sequences that are represented as hidden Markov models, and may be searched with HMMER.

      • Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL (2002). The Pfam protein families database. Nucleic Acids Res. 30(1):276-280
      • Eddy, SR (1998) Profile hidden Markov models. Bioinformatics 14:755-63

        HMMER is governed by the GNU Public License

      PSI-BLAST
      PSI-BLAST is a method for detecting sequence homologs of a given protein. It uses the concept of searching with a position-specific residue substitution profile appropriate to the family in which the query belongs. This allows for more sensitive detection of remote homologous sequences. Robetta runs PSI-BLAST 2.2.6 locally.

      • Schaffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, Koonin EV, Altschul SF. (2001) Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res. 29(14):2994-3005.
      • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25(17):3389-402

      PsiPred
      PsiPred is a secondary structure prediction method that uses feed-forward neural networks and PSI-BLAST.

      • Jones DT. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292: 195-202.

      Reply Email
      An optional email address that your results will be mailed to.

      SAM-T99
      Target99 is a secondary structure prediction method that is part of the SAM package.

      • Karplus K, Barrett C, Hughey R. (1998) Hidden Markov Models for detecting Remote Protein Homologies. Bioinformatics 14(10):846-56
      • Park J, Karplus K, Barrett C, Hughey R, Haussler D, Hubbard T, Chothia C. (1998) Sequence Comparisons Using Multiple Sequences Detect Three Times as Many Remote Homologues As Pairwise Methods. J Mol Biol 284(4):1201-10

      StrAD-Stack
      StrAD-Stack (STRuctural Alignment of Domains, Stacked) a multiple structural alignment method. It parses the target into its domains structurally using a consensus variant of       Taylor's method for structure-based domain parsing, followed by scanning those domains against a domain database (that have been similarly consensus Taylor parsed) using the structure-structure alignment program 3D-Pair. Statistics for each domain are therefore based solely on domains of similar length and secondary structure composition. The method was developed by Dylan Chivian for use with K*Sync.

      • Chivian D and Baker D. (2006) Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection. Nucleic Acids Res. 34(17):e112

      Taylor's Structure-based Domain Parsing
      Taylor's method for structure-based domain parsing is a fast Ising model based technique and is quite good at discriminating domain-insertion events.

      • Taylor WR. (1999) Protein structural domain identification. Protein Engineering. 12(3):203-16

      TMHMM
      TMHMM is used to identify transmembrane regions. Note: Rosetta is not developed for transmembrane proteins.

      • A. Krogh, B. Larsson, G. von Heijne, and E. L. L. Sonnhammer. "Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes." JMB, 305(3):567-580, January 2001.
      • E. L.L. Sonnhammer, G. von Heijne, and A. Krogh. A hidden Markov model for predicting transmembrane helices in protein sequences. In J. Glasgow, T. Littlejohn, F. Major, R. Lathrop, D. Sankoff, and C. Sensen, editors, Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology, pages 175-182, Menlo Park, CA, 1998. AAAI Press.]

      UW-PDB-BLAST
      UW-PDB-BLAST is a method for detecting homologs with structures in the       PDB by running PSI-BLAST agains the non-redundant protein sequence database for 5 rounds to obtain a residue substitution profile for the target that is then used to detect homologs in the PDB sequence database. Perference is given to PDBs detected directly with a single BLAST round or PDBs detected by an "iterative-loosening" approach with PSI-BLAST. Our version of PDB-BLAST is run interally on the Robetta server. Putative parent PDBs (but not their alignments) that are detected by PDB-BLAST with sufficient confidence are used as starting points for modeling with Robetta's Comparative Modeling protocol.

      • Schaffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, Koonin EV, Altschul SF. (2001) Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res. 29(14):2994-3005.
      • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25(17):3389-402

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