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: 22/02/2008]

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 Advance Access published October 23, 2007 (doi:10.1093/bfgp/elm020)
[PDF]

Lectures, Excercises

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]

. 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]
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.)

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

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]
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

Nucleic-acid containing structures only

Protein structures only

Database of Comparative Protein Structure Models - ModBase

Structure-based classification of proteins

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 Too,s 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)
Sybyl (Tripos)

Free (for academic usage)

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 Accelry Discovery Studio Visualizer
(successor of the Accelrys Viewer) is again
available for free ]
Vega
Visual Molecular Dynamics - VMD
WHATIF
YASARA

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

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 intermediate observed in a 1-microsecond simulation in aqueous solution.
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 link | 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]