Software Updates

Amber

a suite of biomolecular simulation programs. It began in the late 1970's, and is maintained by an active development community.

TomoDRGN

a tool that extends the cryoDRGN framework to cryo-ET by learning heterogeneity from datasets in which each particle is sampled by multiple projection images at different stage tilt angles.

AlphaFold

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

spIsoNet

a tool designed to correct for the preferred orientation problem in cryoEM by self-supervised deep learning, by recovering missing information from well-sampled orientations in Fourier space.

GisSPA

a GPU accelerated program, can translationally and rotationally localize the target protein complex in cellular lamellae, as prepared with a focused ion beam, using single cryo-electron microscopy images without tilt-series, and reconstruct the protein complex at near-atomic resolution.

SBGrid Installer

Boltz-1

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.

RELION

(REgularised LIkelihood OptimisatioN) a stand-alone computer program for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.

cryoDRGN

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.

CryoSegNet

a tool for accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and specialized U-Net

POKY

a software suite for multidimensional NMR and 3D structure calculation of biomolecules.

Vesicle-Picker

is a tool that identifies membrane proteins in cryo-EM micrographs by using the Segment Anything Model and integrating with cryoSPARC.

CcpNmr Analysis

a series of programs for macromolecular NMR including AnalysisAssign, AnalysisScreen, AnalysisMetabolomics and AnalysisStructure, and with version 3, the addition CcpNmr ChemBuild.

ModelAngelo

an automatic atomic model building program for cryo-EM maps.

CCP4

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

POKY

a software suite for multidimensional NMR and 3D structure calculation of biomolecules.

MiLoPYP

a self-supervised molecular pattern mining and particle localization in situ.

Coot

(Crystallographic Object-Oriented Toolkit) an application that supports model building and real space refinement. This application interfaces with refmac, Phenix, and several other applications. Coot was recognized as the best structural biology application in 2008 by SBGrid.