Supported Applications

Description

BindCraft2 (BC2) brings de novo miniproteins, scaffolded binders, cyclic peptides and multistate design into one workflow. Describe your target, choose the kind of binder you want, and add properties that matter for your experiment. Named presets supply the design settings and acceptance filters; you can adjust individual settings when needed.

Usage

Usage Notes

SBGrid curated BindCraft2 exposes one callable program: bindcraft

Available Versions

There are two versions of BindCraft2 available in SBGrid: 1.0.3_cu12 and 1.0.3_cu13

Users should set the version override variable for one of these:

$ source /programs/sbgrid.shrc

$ export BINDCRAFT2_X=1.0.3_cu12

cuda12 needs driver ≥ 525 and compute capability ≥ sm_60 (Maxwell through Hopper and newer)

cuda13 needs driver ≥ 580 and sm_75+ (Turing and newer)

AlphaFold2 Parameters

The required alphafold2 parameters are not included with the SBGrid installation.

Users can download them manually with: bindcraft fetch-weights

This will download the weights to:

$HOME/.cache/bindcraft/alphafold

or, if not found, they will be downloaded automatically upon first run to the same location:

$HOME/.cache/bindcraft/alphafold

The location of the parameters can be set with the env var:

export BINDCRAFT_AF2_PARAMS=/shared_storage/bindcraft2/alphafold

The SBGrid installation also includes a link for the parameters to:

/programs/local/bindcraft2/alphafold

If the parameters are placed there they will be found by bindcraft2. This is the recommended deployment for multi-user systems.

Installation

Citation Note