AlphaFold 3 server

ZOOM links:
PMI Muscle Club (CRB 702, TUE at 12 pm)
Cell Motility Journal Club zoom
(CRB 702, WED at 12 pm)
Lab Meeting zoom (CRB 702, Mon at 4 pm)
UPENN zoom 

Upenn Mail:
Webmail



Databases and general protein resources

Gene repositories

  • ATCC Biological material resource
  • Addgene Plasmid repository
  • Dharmacon Collection of cDNAs and ORFs
  • DNAsu Plasmid repository

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)

 

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

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