Software Updates

LigPlot+

the 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.

Coot

(Crystallographic Object-Oriented Toolkit) 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.

cs2star

A simple utility that wraps around csparc2star.py to convert particle positions from Cryosparc JOB directories into a RELION-ready directory.

POKY

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

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.

AlphaPulldown

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

EMReady

improves the quality and interpretability of cryo-EM maps by local and non-local deep learning

imod2relion

A tool reading IMOD points, obtaining particles' info and generating .star file for RELION.

HKL2MAP

a graphical user-interface for macromolecular phasing.

RNAstructure

a complete package for RNA and DNA secondary structure prediction and analysis.

DiffDock

a state-of-the-art method for molecular docking

deltaVina

is a scoring function for rescoring protein-ligand binding affinity

deltaVinaXGB

is a machine-learning based protein-ligand scoring function.

deepTools

a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). Finally, using such normalized and standardized files, deepTools can create many publication-ready visualizations to identify enrichments and for functional annotations of the genome.

MMseqs2

an ultra fast and sensitive sequence search and clustering suite

DiffDock

a state-of-the-art method for molecular docking

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.

Xplor-NIH

a package for biomolecular structure determination from experimental NMR data combined with known geometric data. Xplor–NIH was derived from XPLOR version 3.851 and contains all of the functionality therein in addition to numerous new features designed to render a highly flexible architecture and foster the rapid and easy development of new functionality.

ShapeMapper2

a completely rewritten version of our ShapeMapper for reading out the results of an RNA chemical probing experiment by massively parallel sequencing that integrates careful handling of all classes of adduct-induced sequence changes, sequence variant correction, basecall quality filters, and quality-control warnings to identify RNA adduct sites.

Julia

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

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.

IMOD

a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections.

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.

BioXTAS RAW

a program for analysis of SAXS data that enables creation of 1D scattering profiles from 2D detector images, standard data operations such as averaging and subtraction, analysis of radius of gyration (Rg) and molecular weight, and advanced processing using GNOM, DAMMIF, and AMBIMETER. It also allows easy processing of inline SEC-SAXS data.

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.

PyMOL

widely used molecular visualization package developed by Warren DeLano, now maintained by Schödinger, LLC. This installation includes official incentive builds of PyMOL.

Careless

merges crystallography data without much physics. It performs scaling, merging, and French-Wilson corrections in a single step by directly inferring structure factor amplitudes from unscaled, unmerged intensities.