Software Updates

XDS

(X-ray Detector Software) a software tool for processing single-crystal monochromatic diffraction data recorded by the rotation method.

OpenMPI

an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available.

CNS

(Crystallography & NMR System) an X-ray crystallography suite used for refinement, phasing, and molecular replacement.

EMAN2

a scientific image processing suite with a particular focus on single particle reconstruction from cryoEM images. EMAN2 is a complete refactoring of the original EMAN1 library and contains the SPARX applications.

R

a free software environment for statistical computing and graphics.

ORCA

an electronic structure program package that is a flexible, efficient, and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules.

EMAN2

a scientific image processing suite with a particular focus on single particle reconstruction from cryoEM images. EMAN2 is a complete refactoring of the original EMAN1 library and contains the SPARX applications.

Protenix

a trainable PyTorch reproduction of AlphaFold 3.

tomotools

a tool that provides scripts for making cryo-electron tomography a bit easier.

CryoSamba

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.

smap

a tool for detecting unlabeled macromolecules in 2D Cryo-EM images of cells that uses high-resolution template matching.

R

a free software environment for statistical computing and graphics.

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.

ColabFold

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

ar-decon

AR-Decon, which stands for correcting Anisotropic Resolution by Deconvolution, is a computational pipeline designed to enhance the quality of three-dimensional maps that suffer from anisotropic resolutions, often resulting from datasets with preferred orientations. By applying advanced deconvolution techniques, AR-Decon corrects these resolution discrepancies, leading to more accurate and isotropic 3D maps.

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.

Geneious

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

Gnuplot

a portable command-line driven graphing utility originally created to allow scientists and students to visualize mathematical functions and data interactively. It has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like CCP4 and Octave.

ATSAS

a program suite for small-angle scattering (SAXS) data analysis from biological macromolecules.

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.

3D Slicer

is a free and open-source platform for analyzing and understanding medical image data.

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.

warp-tm-vis

a tool to visualize template matching results from Warp

HOLE

a program that allows the analysis and visualisation of the pore dimensions of the holes through molecular structures of ion channels.

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.

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.

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.

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.

Volume_Seg_Tool

a tool that utilizes deep learning to perform volumetric electron microscopy image segmentations, both semantic and instance segmentation.

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.

MPicker

a tool for membrane flatten and visualization.

AreTomo3

a multi-GPU accelerated software package that enables real-time fully automated reconstruction of cryoET tomograms in parallel with cryoET data collection.

DAQ Score

a computational tool using deep learning that can estimate the residue-wise local quality for protein models from cryo-Electron Microscopy (EM) maps.

Emap2sec+

a computational tool using deep learning that can accurately identify structures, alpha helices, beta sheets, other(coils/turns) and DNA/RNA, in cryo-EM maps of medium to low resolution.

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.

Global Phasing Suite

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

Warp

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

RCrane

a tool that allows for semi-automated building of RNA structure within Coot.

BindCraft

a user friendly and accurate binder design pipeline.

RECOVAR

a software tool for analyzing different conformations in heterogeneous cryo-EM and cryo-ET datasets. RECOVAR can reconstruct high-resolution volumes, estimate conformational density and low free-energy motions, and automatically identify subsets of images with a particular volume feature.

VMD

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

AF2Complex

a tool for predicting and modeling protein complexes with deep learning.