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a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

a neural network based algorithm for heterogeneous cryo-EM reconstruction. In particular, the method models a continuous distribution over 3D structures by using a neural network based representation for the volume.

an open source library for free energy calculations in molecular systems that works with some of the most popular molecular dynamics engines. Perform free energy calculations as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation-based steered MD.

an open-source model which predicts the 3D structure of proteins, rna, dna and small molecules; it handles modified residues, covalent ligands and glycans, as well as condition the generation on pocket residues.

a suite of programs that allows users to carry out molecular dynamics simulations, particularly on biomolecules. The suite can be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB) with either explicit water or generalized Born solvent models. The independently developed packages work well by themselves, and with Amber itself.

a state-of-the-art method for molecular docking

a deep learning based tool for denoising cryo-ET datasets. It is designed to accept .mrc, .rc and .tif single 3D files, or can accept a sequence of 2D.tf files if a path is provided.

is GPU-Accelerated Python STOPgap for Template Matching for fast template matching (TM) in cryo electron tomograms that is based on TM routines from STOPGAP.

an implementation of the inference pipeline of AlphaFold v2.0 using a completely new model that was entered in CASP14.

a Swiss Army knife of crystallography tools. The installation includes the packages from RAVE, SBIN, X-UTIL, VOIDOO, DEJAVU and SPASM.

And includes the following binaries:

• aconio
• cello
• comap
• crave
• essens
• flood
• lsqman
• mama.debug
• mapman
• mave
• moleman2
• o2d
• oops
• prof
• site2rt
• solex
• ssencs
• xpand