3D-Structure Analysis Tools

H2PDB

      H2PDB is an online protein sequence analysis tool, which can map the amino acid variability within a protein sequence alignment onto a 3D structure . The variability is calculated using the Shannon Entropy equation (H), and it is mapped onto the 3D structure via a B factor. The server requires two inputs: a multiple sequence alignment and a PDB file with the 3D-coordinates of one of the sequences in the alignment. Sequence alignment must be in ClustalW format, and must be edited so that it is ungapped with regard to the sequence for which the 3D coordinates are provided. RES numbering in PDB must be consecutive and without missing or repeated RES numbers.Alignment and PDB files must be in TEXT format.


To use the H2PDB and get more information, please click here.


MSAT

      MSAT(MODELING AND SOLVENT ACCESSIBILITY TOOL) is an online protein sequence analysis tool, which can identify the hydrophobic residues exposed by solvents in protein sequences and compare them with the residues of closely related sequences, so as to provide useful help for selecting the best residues for site-specific mutagenesis. The steps of using the tool are:

  • Models the 3D-structure the of input sequence (query). Models are produced by SCWRL, using a template obtained from a PSI-BLAST search against the PDB database. Model is only built only if the e-value of the sequence template is < 1e-5. If the template identity to the query is > 95% following calculations are carried out over the template. Insertions and deletions are not modeled in this version of the program.

  • Calculates the Fractional Solvent accessibility of the models using NACCESS

  • Outputs a 3D-model of the query, and a multiple sequence alignment of the query and various close orthologues.

To use the MSAT and get more information, please click here.


Citation:

http://imed.med.ucm.es/Tools/pvs.html

http://imed.med.ucm.es/Tools/msat.html