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an application for managing an SBGrid software installation. Users can choose a subset of applications for installation on their laptops or desktops or configure site installations for clusters, servers or cloud resources. This version is the command-line interface. A graphical version is available for download on the SBGrid wiki : https://sbgrid.org/wiki/client_downloads .

is a protein design framework for antibody binder design that leverages structure templates and sequence conditioning in backpropagation-based design through AlphaFold-Multimer. The tool enables format-specific binder design with a modular architecture built around three key modules: Template (prepares target structures and identifies hotspots), Trajectory (designs binder sequences using protein folding models and optimization), and Evaluation (assesses designed binders using various metrics). It includes a command-line interface for VHH (nanobody) binder design and has been experimentally validated with million-scale screening.

a collection of cheminformatics and machine-learning software written in C++ and Python.

a program that enables fast and sensitive comparisons of large structure sets.

a pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Topaz includes methods for micrograph denoising using deep denoising models.

a structure refinement and validation for crystallography and single particle analysis.

an implementation of the inference pipeline of AlphaFold using a completely new model that was entered in CASP14.

(Python-based Hierarchical Environment for INtegrated Xtallography) a software suite for the automated determination of molecular structures using X-ray crystallography and other methods.

(Collaborative Computational Project, Number 4) a collection of programs and associated data and software libraries used for macromolecular structure determination by X-ray crystallography.

is a ChimeraX plugin to predict and visualize isosurface levels for 3D density maps. This tool is based on a 3D-CNN initially developed to predict the isosurface levels of 3D density maps, as required by SIREn. More details about the 3D-CNN and SIREn can be found here.