Software Updates

ChimeraX

a tool of the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. Compared to Chimera, ChimeraX has improved graphics (e.g. interactive ambient shadows); faster handling of large structures (millions of atoms); and a more modern, single-window user interface.

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.

Ais

a tool that provides annotation and segmentation of cryo-ET data using convolutional neural networks.

CUDA

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

Schrodinger

a suite of tools for drug discovery.

CryoAtom

is a software that automatically constructs full-atom 3D structural models of proteins based on cryo-EM density maps and sequence information.

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.

ResMap

(Resolution Map) a Python (NumPy/SciPy) application with a Tkinter GUI. It is an easy to use software package for computing the local resolution of 3D density maps studied in structural biology, primarily electron cryo-microscopy (cryo-EM). ResMap has a both a GUI (window) and a command line interface.

BindCraft

a user friendly and accurate binder design pipeline.

Google Cloud SDK

a set of tools and libraries for interacting with Google Cloud products and services.

checkMySequence

a sequence assignment validation tool for in cryo-EM models

Google Cloud SDK

a set of tools and libraries for interacting with Google Cloud products and services.

checkMySequence

a sequence assignment validation tool for in cryo-EM models

RDKit

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

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.

checkMySequence

a sequence assignment validation tool for in cryo-EM models

REPIC

REliable PIcking by Consensus (REPIC) is a consensus methodology for harnessing multiple cryogenic-electron microscopy (cryo-EM) particle picking algorithms.