AlphaFold was updated to 3.0.1 with new features, improvements to performance and documentation, and many bug fixes. New features include the flags --max_template_date, --diffusion_num_samples, --num_recycles, --num_seeds, and an option to specify MSA and templates as external files instead of inline in the input JSON. See the release for more features and improvements.
AmberTools was updated to version 24, which includes several new features: inclusion of the ABCG2 charge model for GAFF2, the Quick package for Hartree-Fock and DFT electronic structure calculations, with GPU support, and fe-toolkit, an updated package of routines to analyze alchemical free energy calculations, along with many cpptraj updates.
Boltz-1 0.4.1 was updated to include full data processing pipelines and documentation, updated evaluations, including code, results and predictions, and pocket conditioning that allows users to set specific pocket residues in your configs.
CryFold 1.3.2 is new to SBGrid. CryFold automatically constructs full-atom 3D structural models of proteins based on cryo-EM density maps and sequence information. It uses two main stages: the first step predicts the Cα atom coordinates from the density map, and the second step builds the full-atom model by combining the sequence and density map information. Finally, the full-atom model will undergo post-processing to generate the final protein model.
CryoSamba 1 is a new addition to the sbgrid collection. CryoSamba is used for denoising cryo-ET datasets using a deep-learning based approach and accepts .mrc, .rc and .tif inputs.
DeepDeWedge is also new to the collection at version 20250128. DeepDeWedge implements a deep learning method for simultaneous denoising and missing wedge reconstruction in cryogenic electron tomography.
DeepEMhancer 20241203_5f64fe8_cu11 is now available. This latest commit from the deepemhancer git repository on github includes a few bug fixes and CUDA 11.8, which is compatible with newer GPU cards.
DiffDock 1.1.3 includes a fix for a bug causing the atom graph to contain many incorrect atoms, issues with different sequences and order, as well as setting NaNs and Infs in model scores to a small value. A typo was corrected, and initialization files were added to all Python modules. Docker command instructions in the README.md file were also updated.
DomainSeeker is new to SBGrid at version 20250204. DomainSeeker is a tool for identifying protein domains in cryo-ET maps of protein complexes. It uses AlphaFold2-predicted models to divide proteins into domains based on predicted alignment errors and a graph-based algorithm, then fits these domains into segmented density maps. A scoring system is applied to determine the most likely domain for each map.
FPSim2 was updated to release 0.7.3. This release includes a fix to the returned number of results in a top-K search in parallel (results were correct but brought more than K due to parallelization), an added exception SQLA backend can't run on disk searches, and upgrades to deprecated upload-artifact and download-artifact v3 github actions versions with v4.
GAPSTOP(TM) is new at version 0.3. GAPSTOP(TM) is a GPU-Accelerated Python STOPgap for Template Matching (TM) in cryo electron tomograms based on TM routines from STOPGAP.
IMOD 5.1.0 is a major version update and includes extensive changes, with noteworthy additions to Tilt and Tiltalign to perform reconstruction from raw stack images and apply linear scaling and cross validation. Complete release notes are available on the developer website here: https://bio3d.colorado.edu/imod/changes5.1.html
PDBExtract was updated to release 4.2 for both Mac and Linux users with a new architecture that uses python under the hood. The title contains tools and examples for extracting data from many structure determination applications and assembles the data into mmCIF format suitable for wwPDB deposition.
polychrom is another new title at version 0.1.1. Polychrom is a Python library for simulating chromatin dynamics and 3D genome organization using polymer physics models. It provides tools for running molecular dynamics simulations, analyzing chromatin structure, and comparing results with experimental data like Hi-C or imaging.
LucaProt is another new one at version 20241112. LucaProt is a novel deep learning framework that incorporates protein amino acid sequence and structural information to predict protein function.
USF Gerard Utilities was updated to 20250213, an alpha build of Uppsala Software Factory for 64-bit MacOS.
