SBGridTV
an open source protein pocket (cavity) detection algorithm based on Voronoi tessellation. It was developed in the C programming language and is currently available as command line driven program.
a multi-modal foundation model for molecular structure prediction that performs at the state-of-the-art across a variety of benchmarks. Chai-1 enables unified prediction of proteins, small molecules, DNA, RNA, glycosylations, and more.
a high performance soft fork of OpenSSH that can provide significnatly faster throughput for bulk data transfers over a wide range of network paths.
a simple utility that wraps around csparc2star.py to convert particle positions from Cryosparc JOB directories into a RELION-ready directory.
a collection of cheminformatics and machine-learning software written in C++ and Python.
a neural network-based segmentation tool that automates the analysis of cytoskeletal structures in electron microscopy data accurately distinguishing individual filaments and membranes in complex cellular environments.
a tool that predicts the pKa values of ionizable groups in proteins (version 3.0) and protein-ligand complexes (version 3.1 and later) based on the 3D structure.
is a tool for the systematic analysis of compositionally-heterogeneous cryo-EM datasets. MAVEn is designed to work downstream of cryoDRGN, after users have generated a large number of maps (usually 500-1000) systematically sampling the latent space, but can be applied to any ensemble of volumes.
is a cryo‑EM density map sharpening tool that estimates the underlying atomic distribution of a protein from the density map and computes the corresponding radially averaged structure factor and density histogram.
(Particle Estimation for Electron Tomography) a package for aligning and averaging particles in 3-D subvolumes extracted from tomograms. If PEET and IMOD are both installed, most PEET operations are available from the eTomo graphical user interface in IMOD. PEET is written in Matlab and a compiled version is distributed along with the Matlab runtime environment needed to run it.
a RELION 4 tool with support for composite masks
