2012/ FLI - Leibniz Institute for Age Research

 

3D Structures of Biological Macromolecules


 

Course material
compiled by
Jürgen Sühnel
Biocomputing Group | Leibniz Institute for Age Research - Fritz Lipmann Institute | Jena Centre for Bioinformatics

[Last update: 29/05/2012]


Gallery


Review

 

Rolf Hühne, Frank-Thomas Koch and Jürgen Sühnel
A comparative view at comprehensive information resources on three-dimensional structures of biological macro-molecules.
Briefings in Functional Genomics and Proteomics 2007, 6:220-39. (doi:10.1093/bfgp/elm020)
[PDF]


Lectures, Excercises

 

2013/2014

 

Lectures

  • Facts, Tools and Fascination
    [PPT (22.8 Mbytes) | PDF (12.5 Mbytes); version date: 04/01/2013]

  • A Case Study in Structural Bioinformatics: C-H...PI-Interactions in Proteins
    [PPT (3.8 Mbytes) | PDF (1.1 Mbytes); version date: 04/01/2013]

  • Nucleic Acids
    [PPT (8.4 Mbytes) | PDF (6.3 Mbytes); version date: 04/01/2013]

  • Protein Structure Prediction
    [PPT (7.6 Mbytes) | PDF (3.5 Mbytes); version date: 20/01/2013]

  • Drug Research and Design
    [PPT (8.5 Mbytes) | PDF (4.9 Mbytes); version date: 20/01/2013]

  • Atomic and Molecular Orbitals
    [PPT (3.5 Mbytes) | PDF (1.1 Mbytes); version date: 20/01/2013]

 

Excercises

  • Structural Comparison of Proteins
    [PPT (3.0 Mbytes) | PDF (0.8 Mbytes); version date: 14/01/2014]

  • Membrane Proteins
    [PPT (6.3 Mbytes) | PDF (2.7 Mbytes); version date: 27/01/2014]

 

2012/2013

 

Lectures

  • Facts, Tools and Fascination
    [PPT (21.9 Mbytes) | PDF (12.4 Mbytes); version date: 04/01/2013]

  • A Case Study in Structural Bioinformatics: C-H...PI-Interactions in Proteins
    [PPT (3.7 Mbytes) | PDF (1.1 Mbytes); version date: 04/01/2013]

  • Atomic and Molecular Orbitals
    [PPT (3.6 Mbytes) | PDF (1.1 Mbytes); version date: 04/01/2013]

  • Protein Structure Prediction
    [PPT (7.1 Mbytes) | PDF (3.4 Mbytes); version date: 09/01/2013]

  • Drug Research and Design
    [PPT (8.1 Mbytes) | PDF (4.7 Mbytes); version date: 29/01/2013]
(for copyright reasons only accessible between 29/01/2013 and 04/02/2013)
  • Selected Topics: Quantum Chemistry, Molecular Dynamics, Statistical Potentials, Lattice Models
    [PPT (5.5 Mbytes) | PDF (2.2 Mbytes); version date: 29/01/2012]

  • Point Group Determination for Molecules
    [PPT (3.8 Mbytes) | PDF (0.8 Mbytes); version date: 29/01/2013]

 

Excercises

  • Structural Comparison of Proteins (RMSD, Quaternion Appoach, SuperPose Server)
    [PPT (~ 3.0 Mbytes) | PDF (~ 0.8 Mbytes); version date 14/01/2013]
  • Membrane Proteins
    [PPT (~ 6.0 Mbytes) | PDF (~ 2.6 Mbytes); version date 22/01/2013]
  • Floating Point Operations and Benchmarking of Computer Performance
    [PPT (~ 2.0 Mbytes) | PDF (~ 0.2 Mbytes); version date 23/01/2013]

 

2011/2012

 

Single lecture on 29/05/2012

  • Structure Prediction and Modeling of Biological Macromolecules
    [PPT ]

 

Lectures

  • Facts, Tools and Fascination
    [PPT (21.2 Mbytes) | PDF (11.9 Mbytes); version date: 07/12/2011]

  • A Case Study in Structural Bioinformatics: C-H...PI-Interactions in Proteins
    [PPT (3.7 Mbytes) | PDF (1.1 Mbytes); version date: 14/12/2011]

  • Drug Research and Design
    [PPT] (8.2 Mbytes) | PDF (4.7 Mbytes); version date: 21/11/2011](not freely available due to copyright reasons; please send an email message to jsuehnel@fli-leibniz.de if you want to get the file)

  • Protein Structure Prediction
    [PPT (7.5 Mbytes) | PDF (3.6 Mbytes); version date: 11/01/2012]
  • Nucleic Acids
    [PPT (7.5 Mbytes) | PDF (3.6 Mbytes); version date: 18/01/2012]
  • Selected Topics: Quantum Chemistry, Molecular Dynamics, Statistical Potentials, Lattice Models
    [PPT (5.6 Mbytes) | PDF (2.3 Mbytes); version date: 19/01/2012]
  • Atomic and Molecular Orbitals
    [PPT (3.3 Mbytes) | PDF (1.0 Mbytes); version date: 25/01/2012]

 

Excercises

  • Structural Comparison of Proteins (RMSD, Quaternion Appoach, SuperPose Server)
    [PPT (~ 3.0 Mbytes) | PDF (~ 0.8 Mbytes); version date 13/12/2011]
  • Membrane Proteins
    [PPT (5.8 Mbytes) | PDF (2.3 Mbytes); version date: 17/01/2012]

 

 

2010/2011

 

Lectures

  • Facts, Tools and Fascination
    [PPT (21.0 Mbytes) | PDF (12.6 Mbytes); version date: 07/12/2010]

  • A Case Study in Structural Bioinformatics: C-H...PI-Interactions in Proteins
    [PPT (3.7 Mbytes) | PDF (1.5 Mbytes); version date: 13/12/2010]

  • Nucleic Acids
    [PPT (8.9 Mbytes) | PDF (5.6 Mbytes); version date: 04/01/2010]

  • Drug Research and Design
    [PPT] (8.1 Mbytes) | PDF (5.1 Mbytes); version date: 12/01/2011](not freely available due to copyright reasons; please send an email message to jsuehnel@fli-leibniz.de if you want to get the file)

 

  • Protein Structure Prediction
    [PPT (7.2 Mbytes) | PDF (2.8 Mbytes); version date: 12/01/2011]

  • Selected Topics: Quantum Chemistry, Molecular Dynamics, Statistical Potentials, Lattice Models
    [PPT (5.8 Mbytes) | PDF (2.1 Mbytes); version date: 02/02/2011]

  • Chirality
    [PPT (2.9 Mbytes) | PDF (0.5 Mbytes); version date: 02/02/2011]

  • Point Group Determination for Molecules
    [PPT (3.9 Mbytes) | PDF (0.8 Mbytes); version date: 02/02/2011]

  • Gene Ontology
    [PPT (3.7 Mbytes) | PDF (0.7 Mbytes); version date: 02/02/2011]

 

Excercises

  • Structural Comparison of Proteins (RMSD, Quaternion Appoach, SuperPose Server)
    [PPT (~ 3.1 Mbytes) | PDF (~ 0.8 Mbytes); version date 12/01/2010]
  • Membrane Proteins
    [PPT (5.4 Mbytes) | PDF (1.7 Mbytes); version date: 02/02/2011]

 

..............................................................................................................

 

2009

 

Lectures

  • Part 1: Facts, Tools and Fascination
    [PPT (~ 18.9 Mbytes) | PDF (~ 9.6 Mbytes); version date: 12/05/2009]

 

  • Part 2: Nucleic Acids
    [PPT (~ 8.9 Mbytes) | PDF (~ 4.5 Mbytes); version date 16/06/2009]

 

  • Part 3: A Case Study in Structural Bioinformatics: C-H...PI-Interactions in Proteins
    [PPT (~ 3.8 Mbytes) | PDF (~ 0.9 Mbytes); version date: 24/06/2009]

 

  • Part 4: Drug Research and Design
    [PPT (~ 3.8 Mbytes) | PDF (~ 0.9 Mbytes); version date: 01/07/2009] (not freely available due to copyright reasons)

 

  • Part 5: Protein Structure Prediction
    [PPT (~ 3.8 Mbytes) | PDF (~ 0.9 Mbytes); version date: 08/07/2009]

 

Excercises

  • Structural Comparison of Proteins (RMSD, Quaternion Appoach, SuperPose Server)
    [PPT (~ 3.2 Mbytes) | PDF (~ 0.8 Mbytes); version date 14/07/2009]

 

Other

  • A Few Remarks on Gene Ontology
    [PPT (~ 2.7 Mbytes) | PDF (~ 0.7 Mbytes); version date 01/07/2009]

 

..............................................................................................................................

 

2007/2008

 

Lectures

  • Part 1: Facts, Tools and Fascination
    [PPT(~ 18.9 Mbytes) | PDF (~ 9.6 Mbytes); version date: 06/11/2007]

 

  • Part 2: Nucleic Acids
    [PPT (~ 8.9 Mbytes) | PDF (~ 4.5 Mbytes); version date 18/12/2007]

 

  • Part 3: Drug Research and Design
    [PPT (~8.0 Mbytes) | PDF (~ 3.2 Mbytes); version date: 07/01/2008] (not freely available due to copyright reasons)

 

  • Part 4: A Case Study in Structural Bioinformatics: C-H...PI-Interactions in Proteins
    [PPT (~ 3.8 Mbytes) | PDF (~ 0.9 Mbytes); version date: 15/01/2008]

 

  • Part 5: Protein Structure Prediction
    [PPT (~ 6.6 Mbytes) | PDF (~ 2.5 Mbytes); version date: 22/01/2008]

 

  • Part 6: Protein Structure Prediction and Protein Folding
    [PPT (~ 6.6 Mbytes) | PDF (~ 3.2 Mbytes); version date: 22/01/2008]

 

  • Part 7: Critical Assessement of Protein Structure Prediction
    [PPT (~ 8,4 Mbytes) | PDF (~ 4.1 Mbytes); version date: 22/02/2008]

 

Excercises

  • Structural Comparison of Proteins (RMSD, Quaternion Appoach, SuperPose Server)
    [PPT (~ 3.2 Mbytes) | PDF (~ 0.8 Mbytes); version date 19/12/2007]
  • Membrane Proteins
    [PPT ( ~5.0 Mbytes) | PDF (~1.7 Mbytes)]

 

..............................................................................................................................

 

2006

 

Lectures

 

The Jena Library of Biological Macromolecules - JenaLib

  • [PPT (~ 10.9 Mbytes) | PDF (~4.8 Mbytes); version date; 04/12/2006]

 

3D Structures of Biological Macromolecules

  • Part 1: Facts, Tools and Fascination
    [PPT (~ 14.3 Mbytes) | PDF (~ 7.3 Mbytes); version date: 09/05/2006]
  •  

  • Part 2: Nucleic Acids
    [PPT (~8.6 Mbytes) | PDF (~4.8 Mbytes); version date: 14/06/2006]
  •  

  • Part 3: Drug Research and Design
    [PPT (~8.6 Mbytes) | PDF (~4.7 Mbytes); version date: 21/06/2006] (not freely available due to copyright reasons)
  •  

  • Part 4: Protein Structure Prediction
    [PPT (~5.7 Mbytes) | PDF (~2.0 Mbytes); version date: 05/07/2006]
  •  

  • Part 5: Protein Structure Prediction and Protein Folding
    [PPT (~5.7 Mbytes) | PDF (~2.5 Mbytes); version date: 05/07/2006]
  •  

  • Part 6: A Case Study in Structural Bioinformatics: C-H...PI-Interactions in Proteins
    [PPT (~3.8 Mbytes) | PDF (~1.4 Mbytes); version date: 12/07/2006]

 

Excercises

 

......................................................................................................................................................................................

 

2005
  • Part 1: Facts, Tools and Fascination
    [PPT (~ 11.2 Mbytes) | PDF (~ 8.1 Mbytes); version date: 18/05/2005]
  • Part 2: Nucleic Acid Structures
    [PPT (~ 7 Mbytes) | PDF (~ 4.9 Mbytes); version date: 10/06/2005, updated version includes a better description of the orientation of base pairs relative to the minor and major grooves in B-DNA, when seen from top of the double helix]
  • Part 3: Drug Research and Design
    [PPT (~ 6.1 Mbytes) | PDF (~ 4.9 Mbytes); version date: 08/06/2005]  (not freely available due to copyright reasons)
  • Part 4: Protein Structure Prediction - I
    [PPT (~ 3.7 Mbytes) | PDF (~ 1.8 Mbytes); version date: 15/06/2005]
  • Part 5: Protein Structure Prediction - II
    [PPT (~ 4.3Mbytes) | PDF (~ 2.8Mbytes); version date: 22/06/2005]

 


Databases and Web Resources

 

Experimental Methods for 3D Structure Determination of Biological Macromolecules

 

3D Structure Databases

 

Comprehensive resources of biological macromolecules

 

Nucleic-acid containing structures only

 

Protein structures only

 

Structure-based classification of proteins

 

Small molecules

 

Other Databases and Web Resources

 

Molecule Superposition

  • SuperPose (Protein Superposition Server)
  • DaliLite (Pairwise comparison of protein structures)
  • CE - Databases and Tools for 3D Protein Structure Comparison and Alignment Using the Combinatorial Extension Method

 

Secondary Structure Prediction and Fold Recognition (Threading)

 

Ab Initio Structure Prediction

 

General Purpose Structure Prediction

  • Robetta: Full-chain Structure Prediction Server

 

Other

 


Molecular Graphics and Modeling Programs

[some of these programs are primarily devoted to visualization and include only a few additional analysis tools; for others visualization is only a minor part of functionality]

 

Commercial

 

Free (for academic usage)

 


Molecular Dynamics Packages

 

Quantum Chemistry Programs

  • ADF [density functional package for chemists]
  • GAUSSIAN
  • SPARTAN
  • TURBOMOLE [Program package for ab initio Electronic Structure Calculations]

 

Other Programs

  • CURVES [Helical Analysis of irregular nucleci acids]
  • DSSP [Secondary structure determination of proteins from 3D structures]
  • Modeller [Program for comparative protein structure modelling by satisfaction of spatial restraints]
  • PROMOTIF [a program to identify structural motifs in proteins]
  • WHAT_CHECK [protein verification program]

 


Other Information

 


Original Articles and Historical Views

  • Baker D, Sali A.
    Protein structure prediction and structural genomics.
    Science. 2001, 294, 93-96. [PubMed | PDF]
  • Couzin J.
    Breakthrough of the year. Small RNAs make big splash.
    Science. 2002, 298, 2296-2297. [PubMed | PDF]
  • Duan Y, Kollman P. Pathways to a protein folding.
    Science. 1998, 282, 740-744. [PubMed | PDF]
  • Dunitz J.
    Pauling's left-handed alpha-helix.
    Angew. Chem. Int. Ed. 2001, 40, 4167-4173. [PDF]
  • Eisenberg D.
    The discovery of the alpha-helix and beta-sheet, the principal structural features of proteins.
    Proc. Natl. Acad. Sci. USA 2003, 100, 11207-11210. [PubMed | PDF]
  • Huang DB, Vu D, Cassiday LA, Zimmerman JM, Maher LJ 3rd, Ghosh G.
    Crystal structure of NF-kappaB (p50)2 complexed to a high-affinity RNA aptamer.
    Proc Natl Acad Sci U S A. 2003, 100, 9268-9273. [Pubmed | PDF]
  • Korkegian A, Black ME, Baker D, Stoddard BL.
    Computational thermostabilization of an enzyme.
    Science 2005, 308, 857-860. [Pubmed | PDF]
  • Plaxco KW, Dobson CM.
    Time-resolved biophysical methods in the study of protein folding.
    Curr Opin Struct Biol. 1996, 6, 630-636. [Pubmed | PDF]
  • Watson JD, Crick FH.
    Molecular structure of nucleic acids; a structure for deoxyribonucleic acid.
    Nature, 1953, 171, 737-738. [Pubmed | PDF]

 


Books

  • P. E. Bourne, H. Weissig, Eds.: Structural Bioinformatics, Wiley-Liss, 2003, ISBN: 0471201995 [Amazon].
  • C.-I. Branden: Introduction to Protein Structure, Garland Publishing, 2nd edition, 1999, ISBN: 0815323050 [Amazon].
  • A. Lesk: Introduction to Protein Architecture: The Structural Biology of Proteins, Oxford University Press, 2001, ISBN: 0198504748 [Amazon].
  • G. Rhodes: Crystallography Made Crystal Clear, Academic Press, 2000, ISBN: 0125870728 [Amazon].
  • W. Saenger: Principles of Nucleic Acid Structure. Springer-Verlag, 1984. ISBN: 0387907610 [Amazon].
  • G. Steger: Bioinformatik - Methoden zur Vorhersage von RNA- und Proteinstrukturen. Birkhaeuser, 2003, ISBN: 3-7643-6951-5 [Amazon].

 


Last update: July 14, 2009

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