[Biopython] New feature on combining PDB files with 3D molecule files
Natasha Sanjrani <[email protected]> Thu, 30 May 2024 19:47:22 +0100
| Newsgroups | gmane.comp.python.bio.general |
|---|---|
| Message-ID | <[email protected]> |
--===============2063506263523713570== Content-Type: multipart/alternative; boundary="Apple-Mail=_042443FB-67F4-4868-8F5E-D3EF244E339D" --Apple-Mail=_042443FB-67F4-4868-8F5E-D3EF244E339D Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Hi, I have written some code for my PhD in 3D structure-based small molecule = generation to combine protein PDB files with 3D ligand coordinate files = (pdb, sdf, and mol2 formats). I was wondering if this could be = integrated into BioPython as it has been quite helpful for me when = parsing through thousands of molecules and running 3D evaluations on = them with their respective proteins. Please let me know your thoughts on whether this would be useful for = others. The code is linked here: = https://github.com/nsanjrani/prot-lig-combine = <https://github.com/nsanjrani/prot-lig-combine>=20 Kind regards, Natasha= --Apple-Mail=_042443FB-67F4-4868-8F5E-D3EF244E339D Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii <html><head><meta http-equiv=3D"Content-Type" content=3D"text/html; = charset=3Dus-ascii"></head><body style=3D"word-wrap: break-word; = -webkit-nbsp-mode: space; line-break: after-white-space;" = class=3D"">Hi,<div class=3D""><br class=3D""></div><div class=3D"">I = have written some code for my PhD in 3D structure-based small molecule = generation to combine protein PDB files with 3D ligand coordinate files = (pdb, sdf, and mol2 formats). I was wondering if this could be = integrated into BioPython as it has been quite helpful for me when = parsing through thousands of molecules and running 3D evaluations on = them with their respective proteins.</div><div class=3D""><br = class=3D""></div><div class=3D"">Please let me know your thoughts on = whether this would be useful for others. The code is linked = here: <a href=3D"https://github.com/nsanjrani/prot-lig-combine" = class=3D"">https://github.com/nsanjrani/prot-lig-combine</a> </div><d= iv class=3D""><br class=3D""></div><div class=3D"">Kind = regards,</div><div class=3D"">Natasha</div></body></html>= --Apple-Mail=_042443FB-67F4-4868-8F5E-D3EF244E339D-- --===============2063506263523713570== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline _______________________________________________ Biopython mailing list - [email protected] https://mailman.open-bio.org/mailman/listinfo/biopython --===============2063506263523713570==--