Can anyone suggest a tool to construct a contact map between side chain, which displays the probabilities of contact formation for all possible residue pairs inside 1 protein?
One can construct a contact map using charmm software with " COOR DMAT" as keyword. The output file should be re-written in the form of a matrix and then plotted.
You can use www.chemosophia.com for on-line computation of atom-atomic electron overlaps . Just register, upload your system in SDF format, select "Large organic and elementorganic molecular systems" service (the service is available for systems with up to 10 000 atoms) and find there "Fast integration of atomic basins (neglect of high order overlaps) " software. Moreover, you can use "Search for critical points" software for determination of bond critical points and their properties between residues. At least, if your protein system consists less than 1000 atoms you can estimate atom-atomic electron overlaps and visualize atomic boundaries including separatrices using "Integration of atomic basins" software in "Single molecule calculations " service. Now all these computations are available on-line for free.
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