COLORADO3D- Help Webpage

General description

COLORADO-3D is a www-server for protein models evaluation. Several different methods for testing 3D models are used, i.e. VERIFY3D, PROSAII, ANOLEA, PROVE. The residue depth, a parameter proposed by S. Chakravarty and R. Varadarajan as a useful for the analysis of protein structure and stability, was also implemented.

While PROVE is the method that assess protein structure acording to its stereochemical property, namely to the regularity (or irregularity) of the atom volume, Verify3D, ProsaII and ANOLEA are based on the inverse folding approach and evaluate the environment of each residue in a model with respect to the expected environment as found in the high resolution X-ray strutures. Verify3D operates on the "3D-1D profile" of a protein structure, which includes the statistical preferences for the following criteria: the area of the residue that is buried, the fraction of side-chain area that is covered by polar atoms (oxygen and nitrogen) and the local secondary structure. For structures determined by X-ray crystallography, the default option in VERIFY3D is to assess the compatibility of each amino acid residue with the local 3D structure by averaging the 3D-1D score in a window of 21 residues. For protein models we recommend the use of shorter window (5-11 residues). PROSAII relies on empirical energy potentials derived from the pairwise interactions observed in well defined protein structures. This program is more stringent than VERIFY3D, and while regions with small structural errors (such as imperfect pairing of hydrogen bonds in the neighboring beta-strands or poor geometry that does not allow to form a proper salt bridge) can be often acceptable for VERIFY3D (and colored green to light blue by COLORADO3D), PROSAII tends to pin them down and consequently COLORADO3D would highlight them in red. The score reported on ANOLEA combines a pairwise distance-dependent non-local energy term with an accessible surface energy term. It was reported that ANOLEA can identify bona fide errors in models, which were positively validated by VERIFY3D and PROSAII.

Inputing data into program

Program accepts as an input file in the pdb format. Optionally an user can submit the alignment file (together with the pdb file). On the basis of the provided protein sequences there will be created the additional models of the considered protein (by the use of the SCWRL program).

Program sends as an output the PDB-file, with the temperture (B-factor) values replaced by the scores of the assessment method. All the scores are scaled- the well-scored fragments get values between 0.00 and 10.00 (the best value is 0.00), the regions identified as the worst achives values around 90 (the worst value is 99.99). We recommend the use of the visualization program for the analysis of the obtained results. Either the SPDBV or the RasMol can be applied. The well-scored fragments will be coloured in blue and the low-scored protein fragments will be seen as the red/orange ones.


The COLORADO-3D tool operates on the Protein Data Bank (PDB)-formatted files. The file should begin either with the "HEADER" or the "COMPND" record and should be terminated by "END" or "TER" lines. Only the coordinates represented in the ATOM records are taken into account (HETATM records, for instance selenomethionyl residues are ignored!). Other lines, such as REMARK will be ignored too.

The example file can be downloaded here


References

J. M. Sasin, J. M. Bujnicki (2004) COLORADO3D, a web server for the visual analysis of protein structures, Nucleic Acids Res.; 32(Web Server issue):W586-9

F. Melo, E. Feytmans (1998) Assessing Protein Structures with a Non-local Atomic Interaction Energy, J. Mol. Biol., 227, 1141-1152.

F. S. Domingues et al. (2002) Assessing Progress in Structure Prediction, J. Phys. IV

M. J. Sippl (1993) Recognition of errors in three-dimensional structures of proteins, Proteins, 17(4):355-62

M. J. Sippl (1993) Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures, J. Comput. Aided Mol. Des., 7(4):473-501

R. Luthy (1992) Assessment of protein models with three-dimensional profiles, Nature, 356(6364):83-5

S. Chakravarty, R. Varadarajan (1999) Residue depth: a novel parameter for the analysis of protein structure and stability, Structure, 7:723-732

N. Guex, M. C. Peitsch (1997) SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling, Electrophoresis 18, 2714-2723.