AlphaFold 3 server

Databases and General Protein Resources

Molecular Biology and Kinetics Tools

  • ATCC Biological material resource
  • Addgene Plasmid repository
  • Dharmacon Collection of cDNAs and ORFs
  • DNAsu Plasmid repository
  • Tenua Kinetics Simulation Program

Crystallography and Molecular Visualization Software and Databases

Data Processing and Structure Determination

Crystallographic Databases

Protein Sequence and Structure Analysis

Alignment

2D-Structure Analysis

  • DeepCoil Prediction of Coiled Coil
  • Jpred Sequence Analysis and Structure Prediction
  • HCA Hydrophobic Cluster Analysis
  • PairCoil2 Prediction of Coiled Coil
  • PDB2PQR Protein electrostatics

3D-Structure Analysis

  • PPI3D searching, analyzing, modeling protein interactions
  • 3DView pdb viewer
  • iCn3D pdb viewer
  • FirstGlance in Jmol pdb structure analysis
  • 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 three-dimensional structures
  • PISA Interactive tool for the exploration of macromolecular interfaces
  • Phyre2 Protein Homology Recognition Engine
  • Phyre2 (expert mode)
  • PROMALS3D Structure-Based Sequence Alignment
  • RaptorX Protein Structure and Function Prediction
  • SSM Secondary Structure Matching and Protein Structure Comparison
  • LS-align Ligand structural aligment
  • AlphaFold Colab

Synchrotrons and Beamlines

  • APS Argonne National Laboratory(Chicago, IL)
  • BioCARS Bio-Consortium for the Advanced Radiation Source
  • IMCA-CAT Industrial Macromolecular 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)

Cryo-EM facilities

 

UPenn links


Other resources

X-ray Hardware and Crystallization Tools

Scientific Societies

Granting Agencies

  • NIH National Institute of Health
  • NSF National Science Fundation
  • AHA American Heart Assiciation
  • ACS American Cancer Society