Software Updates

Boltz-1

an open-source model which predicts the 3D structure of proteins, rna, dna and small molecules; it handles modified residues, covalent ligands and glycans, as well as condition the generation on pocket residues.

AmberTools

a suite of programs that allows users to carry out molecular dynamics simulations, particularly on biomolecules. The suite can be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB) with either explicit water or generalized Born solvent models. The independently developed packages work well by themselves, and with Amber itself.

CCP4

(Collaborative Computational Project, Number 4) a collection of programs and associated data and software libraries used for macromolecular structure determination by X-ray crystallography.

DiffDock

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

Cryosamba

a deep learning based tool for denoising cryo-ET datasets. It is designed to accept .mrc, .rc and .tif single 3D files, or can accept a sequence of 2D.tf files if a path is provided.

Gapstop(TM)

is GPU-Accelerated Python STOPgap for Template Matching for fast template matching (TM) in cryo electron tomograms that is based on TM routines from STOPGAP.

LipIDens

a pipeline for simulation assisted interpretation of lipid or lipid-like densities in e.g. cryogenic electron microscopy (cryo-EM) structures of membrane proteins.

CryoSieve

an advanced software solution designed for particle sorting/sieving in single particle analysis (SPA) for Cryogenic Electron Microscopy (cryo-EM).

AlphaFold

an implementation of the inference pipeline of AlphaFold v2.0 using a completely new model that was entered in CASP14.

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.

Global Phasing Suite

a program that combines installation of autoPROC, BUSTER, and SHARP available to Global Phasing consortium members.

R

a free software environment for statistical computing and graphics.

USF Gerard Utilities

a Swiss Army knife of crystallography tools. The installation includes the packages from RAVE, SBIN, X-UTIL, VOIDOO, DEJAVU and SPASM.

And includes the following binaries:

• aconio
• cello
• comap
• crave
• essens
• flood
• lsqman
• mama.debug
• mapman
• mave
• moleman2
• o2d
• oops
• prof
• site2rt
• solex
• ssencs
• xpand

Vesicle-Picker

a tool that identifies membrane proteins in cryo-EM micrographs by using the Segment Anything Model and integrating with cryoSPARC.

DeepDeWedge

a tool used for the implementation of a deep learning method for simultaneous denoising and missing wedge reconstruction in cryogenic electron tomography

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.

Focus

an interface for cryo-transmission electron microscopy (cryo-EM) data collection with computer image processing. Focus creates a user-friendly environment to import and manage data recorded by direct electron detectors and perform elemental image processing tasks in a high-throughput manner, while new data is being acquired at the microscope.

pdb_extract

a program suite that contains tools and examples for extracting data from many structure determination applications and assembles the data into mmCIF format for wwPDB deposition.

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.

LucaProt

a novel deep learning framework that incorporates protein amino acid sequence and structural information to predict protein function.

DomainSeeker

a tool designed for de novo identification of protein domains in cryo-ET maps of protein complexes.

CryFold

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