Software Updates

GROMACS

a versatile package that performs molecular dynamics of proteins, lipids and nucleic acids.

OpenFold

a trainable, memory-efficient, and GPU-friendly PyTorch reproduction of DeepMind's AlphaFold 2.

MotionCor2

a multi-GPU program that corrects beam-induced sample motion on dose fractionated movie stacks. It implements a robust iterative alignment algorithm that delivers precise measurement and correction of both global and non-uniform local motions at single pixel level across the whole frame, suitable for both single-particle and tomographic images.

AlphaFold

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

Bsoft

a collection of programs and a platform for the development of software for image processing of electron micrographs, interpretation of reconstructions, molecular modeling, and general image and molecular processing.

Global Phasing Suite

a program that combines installation of autoPROC, BUSTER, and SHARP available to Global Phasing consortium members.

Rosetta

a software suite for modeling macromolecular structures and for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions.

MODELLER

a tool used for homology or comparative modeling of protein three-dimensional structures.

Foldseek

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

crYOLO

a novel automated particle picking software based on the deep learning object detection system 'You Only Look Once' (YOLO). CrYOLO is available as a standalone program under http://sphire.mpg.de/ and is part of the image processing workflow in SPHIRE.

AmberTools

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.

BUSTER

a software system containing crystallographic structure refinement using Bayesian statistical methods (BUSTER), ligand fitting (rhofit) and a fully automated pipeline (Pipedream) to drive a structure based fragment/ligand screening pathway.

TomoTwin-cryoet

a deep metric learning based particle picking procedure for cryo-ET

Geneious

a powerful and comprehensive suite of molecular biology and NGS analysis tools.

cryosparc-tools

a toolkit for interfacing with CryoSPARC.