Hi Tom et al.,

I have Boltz2 running on my local Linux computer. It does rather well with protein folding and co-folding with a protein and small-molecule ligand as long as the ligand is a fairly conventional structure. However, some problems arise with somewhat more exotic structures, such as organophosphorus compounds with chiral phosphorus and/or P=S moieties, which tend to end up as P-SH. I have also tried ferrocene derivatives,which are rejected by Boltz2. Some of the issues with ligands arise when converting 3D structure files in SDF format to SMILES. For this, I get better results using RDKit rather than OpenBabel for the conversion.

Best wishes,

Rudy

Rudy J. Richardson, ScD, DABT
Molecular Simulations Laboratory
Room M6065 SPH-II 2029
University of Michigan
1415 Washington Heights
Ann Arbor, MI 48109-2029 USA

Tel: +1-734-936-0769
Fax: +1-734-763-8095

On Mon, Jun 9, 2025 at 5:09 PM Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Lynne,

  I plan on getting Boltz-2 and affinity prediction into ChimeraX probably in late June or July in ChimeraX daily builds.  We are planning to release ChimeraX version 1.10 later this week and it will use Boltz-1.

  I tested Boltz-2 when it was released a few days ago.  While it runs on Mac it produces wrong protein folds and ligands with all atoms on top of each other.  It worked correctly on Linux.  I did not yet try on Windows.  A main purpose of putting Boltz into ChimeraX is so that biology researchers can run it on Mac and Windows computers, so I will need to get Boltz-2 working on those before I put it into ChimeraX.

Tom


On Jun 8, 2025, at 9:51 AM, Lynne Howell via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

thanks for the suggestion … the guys in the lab have already done this but it’s very difficult (if not impossible, given the way the hospital has set up security) to access the workstation in the lab when working off site …. Was hoping to be able to work on this in the weekend 
L

From: Rudy Richardson <rjrich@umich.edu>
Sent: Sunday, June 8, 2025 9:31:48 AM
To: Lynne Howell <howell@sickkids.ca>
Cc: Sherwood Casjens via ChimeraX-users <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] Boltz-2
 
You don't often get email from rjrich@umich.edu. Learn why this is important
Hi, it's also fairly easy to install Boltz-2 in a standalone conda python environment.

Best wishes,

R

Rudy J. Richardson, ScD, DABT
Molecular Simulations Laboratory
Room M6065 SPH-II 2029
University of Michigan
1415 Washington Heights
Ann Arbor, MI 48109-2029 USA

Tel: +1-734-936-0769
Fax: +1-734-763-8095


On Sun, Jun 8, 2025 at 8:56 AM Lynne Howell via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

I’m sure it already on your radar – but would love to see Boltz-2 and its ability to predict binding affinity integrated into ChimeraX – as you did for Boltz-1.

Thanks 

L

 

 

 

P. Lynne Howell

Canada Research Chair (2006-2020)

Senior Scientist, Program in Molecular Medicine The Hospital for Sick Children

Professor, Department of Biochemistry, University of Toronto

 

Office and Mailing address:  

Room 20-9-715 

Peter Gilgan Centre for Research and Learning (PGCRL)

686 Bay St. Toronto ON M5G 0A4

 

Phone: 416-813-5378 (Internal 305378)

 

Web page: https://lab.research.sickkids.ca/howell/

 



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