solvent accebility in PDBID

Question

[gbahramali]

Do you have any tools for solvent accessibility(ACC) that upload of pdb- id and residue number and output of this program is solvent accessibility?

For example I want many pdb id and residue number

1gfo residue number 256-260
1flt1  ....................345-349

.......and then in output

in 1gfo pdb id  residue number:
256=65 ACC
257=190 ACC

Answer 1

[Neilfws]

STRIDE. Old but still good.

[gbahramali]

Thanks for your replying, but I have many pdb file and I want input in one text and also I want some of acc of residue in every pdb file

[Neilfws]

You're welcome and if you care to investigate STRIDE as I suggested, you will find that it does what you want.

[gbahramali]

Hello

Thanks for your reply

I have a question about relative solvent acceptability

I have a two groups with many peptides and I want to calculate average of relative solvent acceptability between two groups and how to compare this groups

[Neilfws]

Create a new question please.

[gbahramali]

I CREATED THANKS

Answer 2

[João Rodrigues]

NACCESS, old(er) but still good! Gives you a per-residue accessibility.

Answer 3

[Jiyao Wang]

You can use iCn3D: https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=1top and click "Analysis > Surface Area". You could also run command line script to get the same information with the Node.js script: https://github.com/ncbi/icn3d/blob/master/icn3dnode/surfacearea.js