Articles Teaching Structural Bioinformatics at the Undergraduate Level

Understanding the basic principles of structural biology is becoming a major subject of study in most undergraduate level programs in biology. In the genomic and proteomic age, it is becoming indispensable for biology students to master concepts related to the sequence and structure of proteins in order to develop skills that may be useful in a wide range of applications. Within this context, this article shows a scheme for teaching structural biology based on hands-on computer approaches, including computational genomics, and structural bioinformatics tools. The students learn to use most of the leading computer programs available for the complete path that goes from sequence to structure and eventually function. During the course, they are taught to build models of proteins based on sequence and structure information. The students are also provided with a critical point of view on automatic procedures and learn to discern between likely and unlikely structures of their final models.

[1]  Teresa K. Attwood,et al.  The Babel of Bioinformatics , 2000, Science.

[2]  Baldomero Oliva,et al.  An automated classification of the structure of protein loops. , 1997, Journal of molecular biology.

[3]  B. Rost.  Twilight zone of protein sequence alignments. , 1999, Protein engineering.

[4]  J. Whisstock,et al.  Protein structural alignments and functional genomics , 2001, Proteins.

[5]  T Reichhardt,et al.  It's sink or swim as a tidal wave of data approaches , 1999, Nature.

[6]  José M. Mas,et al.  Refinement of modelled structures by knowledge-based energy profiles and secondary structure prediction: Application to the human procarboxypeptidase A2 , 2000, J. Comput. Aided Mol. Des..

[7]  Arieh Warshel,et al.  Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs , 1993, J. Comput. Chem..

[8]  C. Sander,et al.  A method to predict functional residues in proteins , 1995, Nature Structural Biology.

[9]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[10]  Leszek Rychlewski,et al.  Improving the quality of twilight‐zone alignments , 2000, Protein science : a publication of the Protein Society.

[11]  M. Sippl.  Recognition of errors in three‐dimensional structures of proteins , 1993, Proteins.

[12]  D. Haussler,et al.  Hidden Markov models in computational biology. Applications to protein modeling. , 1993, Journal of molecular biology.

[13]  A. Sali,et al.  Comparative protein structure modeling of genes and genomes. , 2000, Annual review of biophysics and biomolecular structure.

[14]  Arieh Warshel,et al.  Computer Modeling of Chemical Reactions in Enzymes and Solutions , 1991 .

[15]  C. Chothia,et al.  Intermediate sequences increase the detection of homology between sequences. , 1997, Journal of molecular biology.

[16]  Arieh Warshel,et al.  Energetics and Dynamics of Enzymatic Reactions , 2001 .

[17]  José M. Mas,et al.  Statistical Analysis of the Loop-Geometry on a Non-Redundant Database of Proteins , 1998 .

[18]  T. Blundell,et al.  Comparative protein modelling by satisfaction of spatial restraints. , 1993, Journal of molecular biology.

[19]  G. Barton,et al.  Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and residue confidence levels , 1992, Proteins.

[20]  M. Vásquez,et al.  Modeling side-chain conformation. , 1996, Current opinion in structural biology.

[21]  Louis J. Gross.  Education for a Biocomplex Future , 2000, Science.

[22]  Russ B. Altman,et al.  A curriculum for bioinformatics: the time is ripe , 1998, Bioinform..

[23]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[24]  A. Warshel,et al.  Semiquantitative calculations of catalytic free energies in genetically modified enzymes. , 1987, Biochemistry.

[25]  R Sánchez,et al.  Advances in comparative protein-structure modelling. , 1997, Current opinion in structural biology.

[26]  N M Luscombe,et al.  What is Bioinformatics? A Proposed Definition and Overview of the Field , 2001, Methods of Information in Medicine.

[27]  A. Sali,et al.  Protein Structure Prediction and Structural Genomics , 2001, Science.

[28]  J M Thornton,et al.  Validation of protein models derived from experiment. , 1998, Current opinion in structural biology.