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).

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.

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.

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.

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.