Software Updates

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.

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.

Tomcat

is a web-based tool designed for cataloging and managing tomography data. It provides an intuitive interface to browse, view (including low-mag overviews and animations), annotate, and organize tomograms across multiple directories.

RareFold

is a tool for the structure prediction and design of proteins that include non-canonical amino acids. It supports 29 different rare amino acids in addition to the 20 standard ones. The package includes the EvoBindRare framework, which enables the de novo design of both linear and cyclic peptide binders with expanded chemical diversity, without requiring prior knowledge of the target's binding site.

GROMACS

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

VirtualIce

is 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.

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.

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 diffusion model based protein complex structure modeling tool.

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.