I am looking for a bioinformatic way to predict protein structural changes when I acetylate a specific residue of a protein. Any suggestions?
Julie,
You will need to use some software like
http://expasy.org/tools/
http://genomes.urv.es/OPTIMIZER/
http://en.wikipedia.org/wiki/List_of_protein_structure_prediction_software
NetSurfP — Secondary Structure and Surface Accessibility predictor
CASP experiments home page
Structure Prediction Flowchart (a clickable map)
ExPASy Proteomics tools — list of prediction tools and servers
DomPred — London's Global University
DOMpro — University of California Irvine
DomainSplit — University of Pittsburgh
PredictProtein
Protinfo — comparative and de novo protein structure and complex modelling server
SCRATCH Protein structure prediction suite that includes SSpro
PSIPRED The PSIPRED protein structure prediction server
PSSpred A multiple neural network training program for protein secondary structure prediction
Julie,
You will need to use some software like
http://expasy.org/tools/
http://genomes.urv.es/OPTIMIZER/
http://en.wikipedia.org/wiki/List_of_protein_structure_prediction_software
NetSurfP — Secondary Structure and Surface Accessibility predictor
CASP experiments home page
Structure Prediction Flowchart (a clickable map)
ExPASy Proteomics tools — list of prediction tools and servers
DomPred — London's Global University
DOMpro — University of California Irvine
DomainSplit — University of Pittsburgh
PredictProtein
Protinfo — comparative and de novo protein structure and complex modelling server
SCRATCH Protein structure prediction suite that includes SSpro
PSIPRED The PSIPRED protein structure prediction server
PSSpred A multiple neural network training program for protein secondary structure prediction
Dear julie,
You need to use molecular dynamics simulations.MD simulations have provided detailed information on the fluctuations and conformational changes of proteins and nucleic acids.
http://www.ch.embnet.org/MD_tutorial/pages/MD.Part1.html
MD softwares:
http://ambermd.org/
www.gromacs.org/
www.charmm.org/
Dear Julie Ma'am,
Can you tell after acetylation the particular amino acid is changing into what molecule. Based on the type, the method may vary a little. If the resulting residue is some another amino acid then secondary structure prediction (PSIPRED, etc.) and molecular dynamic simulation (gromacs) can be done easily. If the resulting molecule is non-aminoacid then, molecular dynamics simulation can be done with some modifications in protein pdb file, as now the modified residue will be considered as hetero-atom (not aminoacid).
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