AlphaFlow 20241203_86d7606 is new to SBGrid. AlphaFlow is a modified version of AlphaFold, fine-tuned to include a flow matching objective, designed for generative modeling of protein conformational ensembles. It aims to model experimental ensembles, i.e, potential conformational states as they would be deposited in the PDB, and molecular dynamics ensembles at physiological temperatures.
AlphaFold was bumped a couple of releases to version 3.0.0_20241202_aa724ca, which introduces a significantly enhanced architecture utilizing diffusion-based techniques. This model can now forecast the combined structural arrangement of intricate molecular assemblies, encompassing proteins, DNA and RNA molecules, small chemical compounds, ionic species, and chemically altered amino acids.
Avogadro 1.2.0 for Mac is the last in the 1.X series and fixes several issues.
cryoSTAR is new to SBGrid at version 20241104_b64aa39. cryoSTAR is a neural network based framework for recovering conformational heterogeneity of protein complexes from cryo-EM data. By leveraging the structural prior and constraints from a reference pdb model, cryoSTAR can output both the protein structure and density map.
CUDA 12.4, 12.5, and 12.6 were pushed out. The CUDA 12.x series includes performance improvements and minor bug fixes. It also requires Linux driver version >=525.60.13.
EMRNA 1.5 introduces POSIX shell compatibility for Ubuntu systems.
GROMACS was updated to version 2024.2_cu12.2.
ORCA 6.0.1 introduces a new LeanSCF implementation, expanded relativistic calculations, improved solvation models, advanced spectroscopic capabilities, and a Machine-readable property file system.
Relion 5.0.0 was updated to include SBGrid versions 5.0.0_cu12.2 and 5.0.0_cu11.8, the first stable version of RELION 5.0, which includes Blush regularization, DynaMight for modeling continuous structural heterogeneity, ModelAngelo for automated atomic model building, a complete subtomo-gram averaging pipeline, and many other features.
SAMtools 0.1.19_r8 is a rebuild of 0.1.19, a very old release, for Rocky 8.
Tardis-EM 0.3.0 is is another new one. Tardis-EM is a Python-based software for automated segmentation of cytoskeletal structures and membranes from electron microscopy data. It excels in high-throughput instance segmentation of microtubules, membranes, and actin filaments from various EM modalities, supporting multiple file formats and resolution ranges.
TomoDRGN 1.0.0 introduces expanded software compatibility, new analysis tools, and improved performance: NextPYP and WarpTools compatibility with float16 image support, a new analyze_volumes command for real-space volume analysis, and an interactive Jupyter notebook template for 2D/3D data visualization.
TomoTwin 0.9.1 includes an update to the torchtrainer.py routine and a bugfix with updated cuml and pandas versions that addresses an issue where Nearest Neighbors descent was calculated incorrectly.
Vesicle Picker 20241112 is also new to the collection. Vesicle PIcker is an automated tool that combines the Segment Anything Model with cryoSPARC to identify and analyze membrane proteins within vesicles from cryo-EM micrographs. This software bridges the gap between image segmentation and structural biology by enabling efficient detection and classification of vesicle-embedded protein complexes.
