Software Updates

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.

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.

Warp

a set of tools for cryo-EM and cryo-ET data processing including, among other tools: Warp, M, WarpTools, MTools, MCore, and Noise2Map.

Global Phasing Suite

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

RingMapper

a code for performing RING-MaP and PAIR-MaP analysis.

UDock2

an interactive multi-body protein-protein docking software that predicts the geometry of protein interactions through an intuitive real-time docking procedure with on-the-fly scoring

Warp

a set of tools for cryo-EM and cryo-ET data processing including, among other tools: Warp, M, WarpTools, MTools, MCore, and Noise2Map.

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.

BCFtools

a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

SAMtools

(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.

TOMOMAN

a MATLAB package for managing the various preprocessing steps for taking raw data to reconstructed tomograms. TOMOMAN mainly acts as a set of wrapper scripts for external packages, managing the input and outputs of each external module to form a cohesive pipeline.

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.

iMosflm

a data processing application for macromolecular crystallography. iMosflm (Graphical User Interface) and Mosflm (data processing application) are distributed with this package.

MDAnalysis

an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools.

ColabDesign

a tool that makes protein design accessible through Jupyter notebooks by using advanced protein structure prediction models like AlphaFold and TrRosetta for designing novel proteins with targeted structures.

Spyder

is a powerful scientific environment written in Python, for Python, and designed by and for scientists, engineers and data analysts.

MDAnalysis

an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools.

ChimeraX

a tool of the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. Compared to Chimera, ChimeraX has improved graphics (e.g. interactive ambient shadows); faster handling of large structures (millions of atoms); and a more modern, single-window user interface.

R

a free software environment for statistical computing and graphics.

Glow

a versatile markdown tool offering both a text-based user interface (TUI) for interactive browsing and a command-line interface (CLI) for direct manipulation of markdown content.

Protkit

a Python library for structural bioinformatics, protein engineering, and machine learning. It offers tools for file handling, database access, protein representation, structure analysis, property calculation, and geometric operations.

2dx

a package (consisting of a suite of five programs: 2dx_manager, 2dx_image, 2dx_diffraction, 2dx_merger and 2dx_logbrowser) for user-friendly image processing of 2D crystals.

Fourier3D

a program for tomogram binning in Fourier space.

SBGrid Installer

CombFold

a pipeline that predicts the structure of large protein complexes starting from the sequences of chains in the complex, accommodating up to 18,000 amino acids and 32 subunits.

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.

Fourier3D

a program for tomogram binning in Fourier space.

CryoID

a graphical user interface for identification of proteins from cryo-EM maps.

BLAST+

a suite of BLAST (Basic Local Alignment Search Tool) tools that utilizes the NCBI C++ Toolkit with a number of performance and feature improvements over the legacy BLAST applications.

pytom-match-pick

a GPU accelerated python module to significantly improve the speed and sensitivity using template matching to detect macromolecules from tomograms.

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.