AreTomo3 is new to SBGrid. AreTomo3 is multi-GPU accelerated software that integrates MotionCor3, AreTomo2, and GCtfFind into a single package and enables real-time, fully automated reconstruction of cryoET tomograms in parallel with cryoET data collection.
AWS CLI was bumped to 2.16.4.
BioXTAS RAW was updated to version 2.3.0. This version includes support for High DPI plots on MacOS, the DENSS IFT method, which provides an open-source alternative to GNOM for IFTs, and the DENSS PDB2SAS method, which provides an open-source alternative to CRYSOL for predicting scattering profiles from models.
ColabDesign is another new tool at release 1.1.1. ColabDesign provides a jupyter notebook environment for protein design using tools like AlphaFold and TrRosetta.
cryoDRGN 3.3.3 includes direct_traversal to generate interpolations in the conformation latent space between two points, support for RELION 3.1 input files in` parse_pose_star`, `filter_star`, and a new --datadir option in cryodrgn abinit_homo for use with .star files.
CTFFIND5 is a new version of the cisTEM program. CTFFIND5 offers CTF estimation for cryoEM. More details in the publication: CTFFIND5 provides improved insight into quality, tilt and thickness of TEM samples.
DeepETPicker is also new to the SBGrid collection at release 20240103. DeepETPicker is a deep learning based open-source software with a friendly user interface to pick 3D particles rapidly and accurately from cryo-electron tomograms.
Dock is now at release 6.11, and is available via version override for Linux. This update includes bugfixes to dock_dn routines and sets up compilation infrastructure for eventual integration with RDKit.
EM-GAN 20230731 is also new in July. EM-GAN is a computational tool that helps with protein structure modeling from cryo-EM maps by enabling the capture of protein structure information from cryo-EM maps more effectively than from raw maps. It is based on 3D deep learning.
Geneious is now at version 2024.0 and includes support for non-antibody therapeutic peptides, analysis of non-antibody therapeutic peptides and proteins, an easily accessible new Graphs tab, and better support for scFv/bi-specifics using Linker databases.
NAMD 3.0 is the latest update and includes many advantages over NAMD 2.14: a new GPU-resident mode providing very fast dynamics, performance improvements compared to GPU-offload mode, with at least 2x increased speed on a single GPU and at least 7x increased speed for multi-GPU scaling on NVIDIA DGX-A100.
ParaView 5.12.1 was just added to the collection. ParaView is an open source post-processing visualization engine.
STOPGAP is also new at release 0.7.4. STOPGAP is a subtomogram averaging workflow written in MATLAB for performing subtomogram averaging tasks including template matching, high-resolution alignment and averaging, and classification. With 0.7.4 the standalone STOPGAP toolbox is available, providing a minimal MATLAB terminal and full access to STOPGAP toolbox functions, without the need for a MATLAB license.
TOMOMAN 0.9 is the last of our new titles. TOMOgram MANager, is a MATLAB package for managing the various preprocessing steps for taking raw data to reconstructed tomograms. TOMOMAN mainly acts as a set of wrapper scripts for external packages, managing the input and outputs of each external module to form a cohesive pipeline. TOMOMAN works as a standalone MATLAB toolbox without the need for a MATLAB license.
