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Databases and general protein resources
Gene repositories
Lab tools
Crystallography tools
- MATTPROB Matthews Coefficient (Vm) Probability Calculation
- HKL Research X-ray Data Processing
- XDS/XSCALE X-ray Data Processing
- SnB Direct-Methods Software Determination of Crystal Structures
- SHELX Suite of Programs for Crystal Structure Determination
- PHENIX Automated determination of macromolecular structures using X-ray crystallography
- CCP4 Crystallography Software Suite
- Coot Model Building, Validation and Refinement
- SHARP/BUSTER Structure Phasing Software
- Crystallographic Software list
Crystallographic databases
Synchrotrons and beamlines
- APS Argonne National Laboratory(Chicago, IL)
- BioCARS Bio-Consortium for the Advanced Radiation Source
- IMCA-CAT Ind. Macromol. Crystallography Associacion Collaborative Access Team
- BioCAT Biophysics Collaborative Access Team
- Berkley Lab Advanced Light Source (Berkeley,CA)
- CHESS Cornell High Energy Synchrotron Source (Ithaca, NY)
- NSLS II National Synchrotron Light Source (Brookhaven, NY)
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Protein sequence and structure analysis
Alignment
2D-Structure Analysis
- DeepCoil Prediction of Coiled Coil
- Jpred Sequence Analysis and Structure Prediction
- HCA Hydrophobic Cluster Analysis
- PDB2PQR Protein electrostatics
3D-Structure Analysis
- PPI3D searching, analyzing, modeling protein interactions
- DynDom Protein Domain Movement Analysis
- PolyPhen-2 prediction of functional effects of human nsSNPs
- CATH Protein Structure Classification
- Consurf Analysis of Surface Conservation in Protein Structures
- Dali Protein Structure Analysis and Structural Homology Identication
- HHpred Homology Detection and Structure Predictions
- I-TASSER Protein Structure and Function Prediction
- Modeller Homology or comparative modeling of protein 3D structures
- PISA Interactive tool for the exploration of macromolecular interfaces
- Phyre2 Protein Homology Recognition Engine
- Phyre2 (expert mode)
- PROMALS3D Structure-Based Sequence Alignment
- SSM Secondary Structure Matching and Protein Structure Comparison
- AlphaFold Colab
Cryo-EM tools
Cryo-EM facilities
Crystallography hardware
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UPenn links
Other resources
Scientific societies
Granting agencies
- NIH National Institute of Health
- NSF National Science Fundation
- AHA American Heart Assiciation
- ACS American Cancer Society
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