Quartzy - lab management
Benchling - oligo design
Google Calendars

Databases and General Protein Resources

Molecular Biology and Kinetics Tools

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

Crystallography and Molecular Visualization Software and Databases

  • Data Processing and Structure Determination
    • MATTPROB Matthews Coefficient (Vm) Probability Calculation
    • EDS Electron Density Server
    • 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
    • PyMOL Molecular Visualization
    • SHARP/BUSTER - Structure Phasing Software
    • ARP/wARP - Automated Structure Building and Refinement
    • USF Uppsala Structural Biology Resources
  • Crystallographic Databases

Scientific Societies



Protein Sequence and Structure Analysis

  • Alignment
    • Clustal W Multiple Sequence Alignment
    • T-COFFEE Multiple Sequence Alignment
    • ESPript Multiple Sequence Alignment
    • Jalview Multiple Sequence Alignment Editor
  • 2D-Structure Analysis
    • Jpred Sequence Analysis and Structure Prediction
    • HCA Hydrophobic Cluster Analysis
    • Coils Prediction of Coiled Coil
    • PairCoil2 Prediction of Coiled Coil
    • PDB2PQR electrostatics
  • 3D-Structure Analysis
    • PISA Interactive tool for the exploration of macromolecular interfaces
    • HHpred Homology Detection and Structure Predictions
    • CATH Protein Structure Classification
    • Dali - Protein Structure Analysis and Structural Homology Identication
    • SSM Secondary Structure Matching and Protein Structure Comparison
    • Phyre2 Protein Homology Recognition Engine
    • Phyre2 (expert mode)
    • RaptorX Protein Structure and Function Prediction
    • I-TASSER Protein Structure and Function Prediction
    • Consurf¬† Analysis of Surface Conservation in Protein Structures
    • PROMALS3D Structure-Based Sequence Alignment

Synchrotrons and Beamlines

  • NSLS - National Synchrotron Light Source (Brookhaven, NY)
  • CHESS Cornell High Energy Synchrotron Source (Ithaca, NY)
  • APS Argonne National Laboratory (Chicago, Illinois)
    • BioCARS Bio-Consortium for the Advanced Radiation Source
    • IMCA-CAT Industrial Macromolecular Crystallography Associacion Collaborative Access Team
    • BioCAT - Biophysics Collaborative Access Team

X-ray Hardware and Crystallization Tools

UPenn links

Granting Agencies

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