SCit: Tools for protein side chain conformation analysis and editing
This server provides several tools for the analysis, quality assessment and editing of protein side chain conformations.
One feature of this series of tools is that is makes
use of a Hidden Markov Model derived Structural Alphabet.
More information on HMM structural alphabets here.
More information on SA derived rotamers here.
SCit users guide:
The SCit main page can provide several services at one time:
- Load a PDB file for further processing.
- Automatically (re)build side chains for which some or all heavy atoms are missing
Note that, at this stage, it simply consists in the building of side chains in a standard conformation. Further repositioning is possible using the next stage tools.
- Substitute side chains, if a sequence is specified
- (Re)position side chains corresponding to the uppercase letter of the
The main page accepts as parameters:
After processing, you can enter a more specific series of tools.
It contains several information about the file you loaded and proposes a
series of actions, which we hope are rather self comprehensive.
Some information about how to use each service is given below. Depending
on the ongoing work, their interface may vary slightly.
- PDB file: a PDB formatted protein structure.
For RMN structures, only the first model is currently considered.
The program checks the backbone geometry: incorrect geometry or backbone missing atoms may be not compatible with the HMM encoding. In such case, the program will stop. Another check is related to the presence of all side chain heavy atoms.
- A sequence (Optional): The specified sequence length MUST exactly match that of the PDB file. It will be used to
Subsitute amino acids not matching the PDB file sequence.
(re)Position the side chains. For such purpose, only parts of the sequence specified in upercase will be considered. Lowercase letters of the sequence will remain unaffected.
SCit second stage services:
An example of a typical second stage form is below: