Software Updates

Rosetta

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

R

a free software environment for statistical computing and graphics.

PEET

(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.

RStudio

an integrated development environment (IDE) for R that includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.

R

a free software environment for statistical computing and graphics.

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.

PEET

(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.

R

a free software environment for statistical computing and graphics.

RStudio

an integrated development environment (IDE) for R that includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.

ColabFold

an easy-to-use Notebook based environment for fast and convenient protein structure predictions.

Avogadro

an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.

IMP

(Integrative Modeling Platform) a program designed to allow mixing and matching of existing modeling components as well as the easy addition of new functionality.

MemBrain-Seg

a tool for membrane segmentation in 3D for cryo-electron tomography (cryo-ET).

cryosparc-tools

a toolkit for interfacing with CryoSPARC.

RoseTTAFold-All-Atom

a biomolecular structure prediction neural network that can predict a broad range of biomolecular assemblies.

MGLTools

a software package for visualization and analysis of molecular structures comprising AutoDockTools (ADT): a graphical front-end for setting up and running AutoDock; Python Molecule Viewer (PMV); and Vision: a visual-programming environment for building networks describing novel combinations of computational methods and yielding new visualizations of their data.

IMP

(Integrative Modeling Platform) a program designed to allow mixing and matching of existing modeling components as well as the easy addition of new functionality.

POKY

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

NMRPipe

a set of comprehensive facilities for Fourier processing of spectra in one to four dimensions, as well as a variety of facilities for spectral display and analysis. This is the official NMRScience version of NMRPipe.

Jalview

a multiple sequence alignment editor written in Java. It is used widely in a variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain database) but is available as a general purpose alignment editor.

DIALS

(Diffraction Integration for Advanced Light Sources) a software project for the analysis of crystallographic diffraction images for many new methods from shutterless, fine-sliced rotation scans to randomly-oriented snapshots of serial crystallography. It uses multiple CPU and GPU machines to increase speed and accuracy based on a comprehensive physical model.

XDSGUI

a GUI (graphical user interface) for XDS designed to help both novice and experienced users; it enables XDS data processing without the command line and supplies additional graphical information in a simple, user-modifiable and user-extensible way. It graphically displays the ASCII and cbf files that XDS writes and can run useful shell commands with a simple mouse click.

IGV

(Integrative Genomics Viewer) a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

IMOD

a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections.

IMP

(Integrative Modeling Platform) a program designed to allow mixing and matching of existing modeling components as well as the easy addition of new functionality.

PHENIX

(Python-based Hierarchical Environment for INtegrated Xtallography) a software suite for the automated determination of molecular structures using X-ray crystallography and other methods.

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.

LipIDens

a pipeline for simulation assisted interpretation of lipid or lipid-like densities in e.g. cryogenic electron microscopy (cryo-EM) structures of membrane proteins.