solvent accebility in PDBID
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9.8 years ago
gbahramali ▴ 20

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
pdb • 2.6k views
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9.8 years ago
Neilfws 49k

STRIDE. Old but still good.

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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

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

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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

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Create a new question please.

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I CREATED THANKS

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9.8 years ago
João Rodrigues ★ 2.5k

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

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2.5 years ago
Jiyao Wang ▴ 370

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

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