Software Updates

BindCraft

Simple binder design pipeline using AlphaFold2 backpropagation, MPNN, and PyRosetta. Select your target and let the script do the rest of the work and finish once you have enough designs to order!

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.

Coot

(Crystallographic Object-Oriented Toolkit) an application that supports model building and real space refinement. This application interfaces with refmac, Phenix, and several other applications. Coot was recognized as the best structural biology application in 2008 by SBGrid.

AlphaPulldown

a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer.

MiLoPYP

a self-supervised molecular pattern mining and particle localization in situ.

Schrodinger

a suite of tools for drug discovery. The Schrodinger suite runs on Linux and Mac workstations, but due to its size, it is not included in our default installation.

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.

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.

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.

EMRNA

a deep learning based automated RNA modeling from cryo-EM maps.

Tardis

a neural network-based segmentation tool that automates the analysis of cytoskeletal structures in electron microscopy data accurately distinguishing individual filaments and membranes in complex cellular environments.

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.

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.

CryoSTAR

a neural network based framework for recovering conformational heterogenity of protein complexes.

Coot

(Crystallographic Object-Oriented Toolkit) an application that supports model building and real space refinement. This application interfaces with refmac, Phenix, and several other applications. Coot was recognized as the best structural biology application in 2008 by SBGrid.

TomoTwin-cryoet

a deep metric learning based particle picking procedure for cryo-ET

FuDA

(Function and Data Analysis) a program whose nmrPipeFit component is designed to analyse nD (n>1) NMR correlation spectra. The program is currently designed for arrayed 2D spectra, such as relaxation experiments and diffusion experiments, and simple 2D and 3D spectra.

AlphaFlow

a modified version of AlphaFold, fine-tuned with a flow matching objective, designed for generative modeling of protein conformational ensembles.

CUDA

a tool that helps redistributable software libraries to support CUDA applications for Linux.

AlphaFold

an implementation of the inference pipeline of AlphaFold v2.0 using a completely new model that was entered in CASP14.

DRGN-AI

a neural network-based algorithm for ab initio heterogeneous cryo-EM reconstruction.