Ultra-fast, coarse-grained molecular dynamics (MD)
a trainable PyTorch reproduction of AlphaFold 3.
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 .
a deep-learning software package for simultaneous missing wedge correction, denoising, and CTF correction in cryo-electron tomography reconstructions using a deep neural network trained on information from the original tomogram(s).
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 de novo modeling protocol to build an entire protein 3D model directly from near-atomic (up to about 5 Angstrom) resolution EM map.
(Collaborative Computational Project, Number 4) a collection of programs and associated data and software libraries used for macromolecular structure determination by X-ray crystallography.
