Software Updates

RDKit

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

DenoisET

is an implementation of the Noise2Noise algorithm specifically designed for cryoET data denoising. The software streamlines integration with AreTomo3 and provides automated tomogram selection for training and inference transition decisions to avoid overdenoising artifacts. It can operate during live data collection, either applying pre-trained models or training new 3D denoising models from scratch using CTF-deconvolved tomograms.

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.

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.

Xmipp

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

SBGrid Installer

Xmipp

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

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.

IntFold

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.

R

a free software environment for statistical computing and graphics.

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. AITom is originated from the tomominer library, adapted from an extended version of the tomominer library, developed at Alber Lab.

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.