Resources & Tools
A curated set of software, protocols, and pipelines for trainees and collaborators—from structure visualization to prediction to full data-processing workflows.
Data-Processing Pipelines
Reproducible, versioned workflows carrying data from acquisition to final model.
Cryo-EM Processing Pipeline
End-to-end scripted workflow from motion correction through final map sharpening.
Model Building & Validation Workflow
Standardized steps for fitting, real-space refinement, and geometry validation.
Cryo-ET Processing Pipeline
Tilt-series to subtomogram averaging — the tomography counterpart to our single-particle workflow.
Software & Tools
Every application and database referenced across the pipeline pages above, from image processing through model validation and deposition.
ChimeraX
Model visualization, interactive fitting, and figure generation for cryo-EM maps and atomic models.
AlphaFold
Structure prediction used for variant interpretation and as a starting model for fitting.
cryoSPARC
Single-particle processing suite used for classification, refinement, and reconstruction.
Coot
Interactive model building and manual rebuilding against cryo-EM and crystallographic density.
ISOLDE
Interactive, physics-based model rebuilding inside ChimeraX using real-time molecular dynamics flexible fitting.
Phenix
Real-space refinement of atomic coordinates against cryo-EM maps, plus broader crystallographic and validation tools.
Rosetta
Model refinement and structure prediction toolkit used alongside Phenix for real-space refinement.
MolProbity
Geometry and clash validation — bond lengths/angles, Ramachandran, and rotamer outliers.
EMRinger
Map-model validation metric scoring side-chain fit to cryo-EM density independent of the refinement target.
SBCloud
SBGrid's cloud-based training environment — curated software, CPU/GPU resources, and storage for cryo-EM/cryo-ET pipelines.
RELION
Bayesian single-particle refinement and classification suite, also used for subtomogram averaging in cryo-ET.
MotionCor2
Anisotropic beam-induced motion correction for movie-mode cryo-EM detector data.
CTFFIND4
Fast contrast transfer function estimation from cryo-EM micrographs.
Topaz
Neural-network particle picking and denoising for low-contrast cryo-EM images.
ResMap
Local resolution estimation for cryo-EM density maps, without reference to an atomic model.
DeepEMhancer
Deep-learning post-processing that sharpens and denoises cryo-EM maps for interpretation.
IMOD
Tilt-series alignment, tomogram reconstruction, and segmentation toolkit for cryo-ET.
AreTomo
Automated, motion-corrected tilt-series alignment and reconstruction for cryo-ET.
cryoCARE
Deep-learning denoising for cryo-ET tomograms, improving contrast for segmentation and picking.
Dynamo
Subtomogram averaging and classification package for cryo-electron tomography.
PDB
The Protein Data Bank — global repository for depositing and retrieving atomic coordinate models.
EMDB
The Electron Microscopy Data Bank — global repository for depositing and retrieving cryo-EM/cryo-ET density maps.
Lab Protocols & SOPs
Standard operating procedures for common bench and microscopy workflows.
Protein Purification SOP
Step-by-step protocol for expression, extraction, and chromatography purification.
Grid Preparation & Vitrification SOP
Blotting parameters, screening criteria, and troubleshooting for cryo-EM grids.
Lab Notebook & Data Management SOP
Naming conventions, storage locations, and backup practices for raw and processed data.
External & Community Links
Partner networks and community resources beyond the lab.
R25 Training Program
Mentored research training program for the next generation of structural biologists.
Cryo-EM Workshops
Hands-on flagship workshop covering the full cryo-EM pipeline, grid to model.
Capacity Building Programs
SBGrid's CryoEM Train-the-Trainer program and BioStruct-Africa's structural biology workshops — both with Dr. Davis's involvement.