3D Structures of Biological Macromolecules

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]

• Jmol-based 3D Structure Tutorials (Interactive Concepts in Biochemistry, Copyright 2006, John Wiley & Sons Publishers, Inc.)

Other

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

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]

• Jmol-based 3D Structure Tutorials (Interactive Concepts in Biochemistry, Copyright 2006, John Wiley & Sons Publishers, Inc.)

• 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

• Structural Comparison of Proteins (RMSD, Quaternion Appoach, SuperPose Server)
• Jmol-based 3D Structure Tutorials (Interactive Concepts in Biochemistry, Copyright 2006, John Wiley & Sons Publishers, Inc.)

• 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

• Crystallography Made Crystal Clear (G. Rhodes)
• X-ray Tutorial (B. Rupp)
• X-ray Crystallography in 5041 Seconds (M. S. Weiss)

3D Structure Databases

Comprehensive resources of biological macromolecules

• Protein Data Bank (PDB)
• PDBsum
• Macromolecular Structure Data Base (MSD)
• OCA
• Jena Library of Biological Macromolecules (JenaLib)

Nucleic-acid containing structures only

• Nucleic Acid Database (NDB)
• RNA Structure Database (RNAbase)

Protein structures only

• Database of Comparative Protein Structure Models - ModBase

Structure-based classification of proteins

• CATH
• SCOP

Small molecules

• National Cancer Institute 3D structure database (collection of 3D structures for over 400,000 drugs)
• Cambridge Structural Database (CSD) (organic and metal-organic compounds including polypeptides and polysaccharides up to 24 units)

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)

• Chou-Fasman Secondary Structure Prediction
• Jpred - A Consensus Secondary Structure Prediction Server
• PredictProtein - Structure Prediction and Sequence Analysis (includes GenThreader)
• PSIPRED (Protein Structure Prediction Server)
• 3D-PSSM (Fold Recognition Server)
• PHYRE (3D-PSSM Successor)

Ab Initio Structure Prediction

• HMMSTR/Rosetta Server

General Purpose Structure Prediction

• Robetta: Full-chain Structure Prediction Server

Other

• Non-canonical Base Pair Database

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

• InsightII (Accelrys; [no longer maintained, replaced by the Discovery Studio Suite )
• Sybyl (Tripos)

• Chime [Web browser plugin]
• Jmol [Interactive web browser applet and standalone program]
• RasMol
• MolScript
• MolMol
• CHIMERA
• NAMOT [Nucleic Acid MOdeling Tool]
• PREPI
• PyMOL
• Raster3D [set of tools for generating high quality raster images of proteins or other molecules]
• RIBBONS
• Swiss PDB Viewer
• Accelrys Viewer Lite [This viewer was originally provided by Accelrys for free, but they have stopped this service. Here you can download versions 4.0 and 5.0]. [I have learned recently, that the Accelrys Discovery Studio Visualizer (successor of the Accelrys Viewer) is again available for free.]
• Vega
• Visual Molecular Dynamics - VMD
• WHATIF
• YASARA

Molecular Dynamics Packages

• AMBER
• CHARMM
• GROMOS
• TINKER

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

• Critical Assessment of Techniques for Protein Structure Prediction - CASP
• Structural Biology Nobel Prizes
• The Very First Biopolymer 3D Structures
• Amino Acid Repositories
• JenaLib
• NIST [see for example the entry page for alanine]
• Berlin Free University
• Birkbeck (School of Crystallography)
• EMBL (Russell Group)
• John Kyrk
• IMB Jena Image Library of Biological Macromolecules Celebrates 50 Years of DNA Double Helix Structure - Poster [PDF]
• PNAS Classics - Protein Structure
• Folding@Home
• Protein-nucleic acid complex [434 CRO PROTEIN COMPLEX WITH 20 BASE PAIR PIECE OF DNA CONTAINING THE OPERATOR OR1, PDB code: 3cro]
  • PDB file
  • Atlas pages
    • PDB
    • PDBj
    • PDBsum
    • MSD
    • OCA
    • NDB
    • JenaLib

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].