Software Updates

MemBrain-Seg

a tool for membrane segmentation in 3D for cryo-electron tomography (cryo-ET).

pytom-match-pick

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

TomoDRGN

a tool that extends the cryoDRGN framework to cryo-ET by learning heterogeneity from datasets in which each particle is sampled by multiple projection images at different stage tilt angles.

crYOLO

a novel automated particle picking software based on the deep learning object detection system 'You Only Look Once' (YOLO). CrYOLO is available as a standalone program under http://sphire.mpg.de/ and is part of the image processing workflow in SPHIRE.

CrystFEL

a suite of programs for processing diffraction data acquired "serially" in a "snapshot" manner, such as when using the technique of Serial Femtosecond Crystallography (SFX) with a free-electron laser source.

MAFFT

a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <200 sequences), FFT-NS-2 (fast; for alignment of <30,000 sequences).

Doppio

a new web-based user interface for CCP-EM and RELION software.

RDKit

a collection of cheminformatics and machine-learning software written in C++ and Python.

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.

MAFFT

a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <200 sequences), FFT-NS-2 (fast; for alignment of <30,000 sequences).

Xmipp

(X-Window-based Microscopy Image Processing Package) a suite of image processing programs primarily aimed at single-particle 3D electron microscopy.

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.

PSI4

is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of molecular properties.

R

a free software environment for statistical computing and graphics.

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.

Unicycler

an assembly pipeline for bacterial genomes.

Volume_Seg_Tool

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

cryoDRGN-AI

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

rs-station_abismal

is f scaling and merging for large diffraction datasets using stochastic variational inference and deep learning.

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.

UGENE

a free open-source bioinformatics software for macOS, and Linux.

RDKit

a collection of cheminformatics and machine-learning software written in C++ and Python.

DenoisET

an implementation of the Noise2Noise algorithm specifically designed for cryoET data denoising.

AreTomo3

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

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.

POKY

a software suite for multidimensional NMR and 3D structure calculation of biomolecules.

Julia

a flexible dynamic language appropriate for scientific and numerical computing with performance comparable to traditional statically-typed languages.

BioEmu

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

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.

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.

SBGrid Installer

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.

IntelliFold

a controllable foundation model for general and specialized biomolecular structure prediction that supports proteins, nucleic acids, and their complexes.

Schrodinger

a suite of tools for drug discovery.

FoldBench

a comprehensive all-atom benchmark for biomolecular structure prediction that spans proteins, nucleic acids, ligands, and six major interaction types.

LigPlot+

a successor to the original LIGPLOT program for automatic generation of 2D ligand-protein interaction diagrams. It is run from an intuitive java interface which allows on-screen editing of the plots via mouse click-and-drag operations.

OpenMM

a high performance toolkit for molecular simulation that can be used either as a stand-alone application for running simulations or as a library you call from your own code.

IPA

a program for ab initio phase determination.

AITom

an open-source platform for AI driven cellular electron cryo-tomography analysis.

Schrodinger

a suite of tools for drug discovery.

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.

cryoPROS

a computational framework specifically designed to tackle misalignment errors caused by preferred orientation issues in single-particle cryo-EM.

PowerFit

a Python package and simple command-line program to automatically fit high-resolution atomic structures in cryo-EM densities.