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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
    • 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

Granting Agencies

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

 

 

UPenn links

Protein Sequence and Structure Analysis

  • Alignment
    • Clustal W Multiple Sequence Alignment
    • ESPript Multiple Sequence Alignment
    • Jalview Multiple Sequence Alignment Editor
    • T-COFFEE Multiple Sequence Alignment
    • SCORECONS A program to score residue conservation in a multiple sequence alignment
    • SIAS Sequence Identity And Similarity
  • 2D-Structure Analysis
    • Coils 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
    • 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

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)

X-ray Hardware and Crystallization Tools