Software Updates

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.

MMseqs2

an ultra fast and sensitive sequence search and clustering suite

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.

Schrodinger

a suite of tools for drug discovery.

Warp

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

PyCoAn

is a Python-based framework for analyzing electron microscopy data within a unified, Matlab-like environment. The package provides a distinctive correlation-based docking methodology that uses cross-validation to define confidence intervals for solutions. It also includes tools for denoising, segmentation, and pattern recognition, and is designed to integrate numerous external data-processing packages through a single interface.

Vina-CUDA

Vina-CUDA, QuickVina2-CUDA, and QuickVina-W-CUDA based on Vina-GPU 2.1, QuickVina2-GPU 2.1, and QuickVina-W-GPU 2.1 further enhance Vina-GPU 2.1 and its variants docking speed by optimizing its core algorithms through deep utilization of GPU hardware features, thereby reducing the cost of virtual screening and increasing the efficiency of drug design.

NAMD

a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

Vesicle-Picker

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

SBGrid Installer

ColabFold

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

XDS

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

Durin

a XDS plugin for reading HDF5 files following the NeXuS format or those written by Dectris Eiger detectors.

Scipion

an image processing framework to obtain 3D models of macromolecular complexes using 3D EM that allows you to execute workflows combining different software tools, while taking care of formats and conversions.

pytom-match-pick

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

Dynamo

a software environment for subtomogram averaging of cryo-EM data.

BioEmu

is a model that samples from the approximated equilibrium distribution of structures for a protein monomer, given its amino acid sequence.

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.

Topaz

a pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Topaz includes methods for micrograph denoising using deep denoising models.

CryoTransformer

a powerful and accurate particle-picking framework using Residual Network (ResNet) and Transformer.

CCPEM-pipeliner

an integrated suite of software tools for processing single particle cryoEM data, from preprocessing raw image data through building and fitting atomic models.

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.

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.

R

a free software environment for statistical computing and graphics.

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.

Topaz

a pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Topaz includes methods for micrograph denoising using deep denoising models.

LigandMPNN

a deep learning-based tool for designing protein sequences conditioned on atomic context, including ligands, DNA, RNA, and modified amino acids.

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.

LocScale

is an automated tool for physics-informed cryo-EM map optimisation (sharpening/density modification), improving interpretability using electron scattering properties derived from the map or an atomic model.

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.

TomCat

a web-based tool designed for cataloging and managing tomography data providing an easy way to view, annotate, and organize tomograms.

RareFold

a tool for the structure prediction and design of proteins that include non-canonical amino acids.

GROMACS

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

VirtualIce

a feature-rich half-synthetic cryoEM micrograph generator that uses buffer cryoEM micrographs with junk and carbon masked out as real background.

R

a free software environment for statistical computing and graphics.

cryosparc-tools

a toolkit for interfacing with CryoSPARC.

RFdiffusion

an open source method for structure generation, with or without conditional information (a motif, target etc). It can perform a whole range of protein design challenges.

DiffModeler

a computational tool using a diffusion model to automatically build full protein complex structure from cryo-EM maps at 0-20A resolution.

PyMOL

a widely used molecular visualization package developed by Warren DeLano, now maintained by Schödinger, LLC. This installation includes official incentive builds of PyMOL.

CryoREAD

a computational tool using deep learning to automatically build full DNA/RNA atomic structure from cryo-EM map.

RosEM

a tool that provides easy access to the rosetta cryoem refinement protocol. The pipeline automates testing of different density weights, use of reference/starting model restraints and selections.

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.

PyEM

a set of Python modules and command-line utilities for electron microscopy of biological samples.

qFit

a collection of programs for modeling multi-conformer protein structures.