Syllabus & Schedule [TEXT] [PDF]
REVISED DEADLINE! Final Exam Papers, as well as All Lab Writeups
for the Course are Due by the Afternoon of Wednesday, December 19th.
Questions for the Exam [PDF]
Understanding Noncovalent Interactions: Ligand Binding Energy and
Catalytic Efficiency from Ligand-Induced Reductions in Motion within
Receptors and Enzymes, D. H. Williams, E. Stephens, D. P. O 'Brien and M. Zhou,
Angewandte Chemie International Edition, 43, 6596-6616 (2004)
[PDF]
Approaches to the Description and Prediction of the Binding Affinity of
Small-Molecule Ligands to Macromolecular Receptors, H. Gohlke and G. Klebe,
Angewandte Chemie International Edition, 41, 2644-2676 (2002)
[PDF]
The Statistical-Thermodynamic Basis for Computation
of Binding Affinities: A Critical Review,
M. K. Gilson, J. A. Given, B. L. Bush and J. A. McCammon,
Biophysical Journal, 72, 1047-1069 (1997)
[PDF]
Calculation of Protein-Ligand Binding Affinities, M. K. Gilson and
H.-X. Zhou,
Annual Reviews in Biophysics and Biomolecular Structure, 36,
21-42 (2007)
[PDF]
Lecture 1 (Aug 30): Overview of Computational Biochemistry [PDF]
Lecture 2 (Sep 4): Molecular Mechanics Energy Functions [PDF]
Lecture 3 (Sep 6): Electrostatics and Polarization [PDF]
Lecture 4 (Sep 11): Treatment of Solvation Effects [PDF]
Lecture 5 (Sep 13): Minimization Algorithms [PDF]
Lecture 6 (Sep 18): Basics of Molecular Orbital Theory [PDF]
Lecture 7 (Sep 25): Monte Carlo Techniques [PDF]
Lecture 8 (Sep 27): Molecular Dynamics Techniques [PDF]
Lecture 9 (Oct 2): Computation of Properties from Simulation [PDF]
Lecture 10 (Oct 4): Navigating Potential Energy Surfaces
Lecture 11 (Oct 9): Theory of Free Energy Computations [PDF]
Lecture 12 (Oct 11): Applications of Free Energy Computations [PDF]
Lecture 13 (Oct 16): Introduction to Docking and Ligand Binding [PDF]
Lecture 14 (Oct 18): Structure Determination via Distance Geometry [PDF]
Lecture 15 (Oct 23): Proteins as Molecular Systems [PDF]
Lecture 16 (Oct 25): Template-Based Modeling of Protein Structure [PDF]
Lecture 17 (Oct 30): QSAR and 3-D QSAR [PDF]
Lecture 18 (Nov 1) Pharmacophore Active Site Modeling [PDF]
Lecture 19 (Nov 6): Molecular Recognition: The Devil's in the Details! [PDF]
Lecture 20 (Nov 8): Protein Structure Prediction I [PDF]
Lecture 21 (Nov 13): Protein Structure Prediction II [PDF]
Lecture 22 (Nov 15): Protein Structure Prediction II
Lecture 23 (Nov 20): GPCR Modeling [PDF]
Lecture 24 (Nov 27): Chemoinformatics [PDF]
Lecture 25 (Nov 29): Structure-Based Drug Design [PDF]
Lecture 26 (Dec 4): Experimental Design [PDF]
Lecture 27 (Dec 6): Superoxide Dismutase Mimetics [PDF]
Biomolecular Modeling: Goals, Problems, Perspectives,
W. F. van Gunsteren, D. Bakowies, R. Baron, I. Chandrasekhar, M. Christen,
X. Daura, P. Gee, D. P. Geerke, A. Glattli, P. H. Hunenberger,
M. A. Kastenholz,
C. Oostenbrink, M. Schenk, D. Trzesniak, N. F. A. van der Vegt
and H. B. Yu,
Angewandte Chemie International Edition, 45, 4064-4092 (2006)
[PDF]
Protein Force Fields, J. W. Ponder and D. A. Case,
Advances in Protein Chemistry, 66, 27-85 (2003)
[PDF]
Monte Carlo and the MANIAC, H. L. Anderson,
Journal of Statistical Physics, 43, 731-748 (1986)
[PDF]
Perspective on Monte Carlo Methods, W. L. Jorgensen,
Theoretical Chemistry Accounts, 103, 225-227 (2000)
[PDF]
The Statistical-Thermodynamic Basis for Computation
of Binding Affinities: A Critical Review,
M. K. Gilson, J. A. Given, B. L. Bush and J. A. McCammon,
Biophysical Journal, 72, 1047-1069 (1997)
[PDF]
Calculation of Protein-Ligand Binding Affinities, M. K. Gilson and
H.-X. Zhou,
Annual Reviews in Biophysics and Biomolecular Structure, 36,
21-42 (2007)
[PDF]
Compensating Enthalpic and Entropic Changes Hinder Binding Affinity Optimization,
V. Lafont, A. A. Armstrong, H. Ohtaka, Y. Kiso, L. M. Amzel and E. Freire,
Chemical Biology & Drug Design, 69, 413-422 (2007)
[PDF]
Motifs for Molecular Recognition Exploiting Hydrophobic Enclosure in
Protein-Ligand Binding, T. Young, R. Abel, B. Kim, B. J. Berne and R. A. Friesner,
Proceedings of the National Academy of Sciences USA, 104, 808-813 (2007)
[PDF]
Target-Related Applications of First Principles Quantum Chemical
Methods in Drug Design, A. Cavalli, P. Carloni and M. Recanatini,
Chemical Reviews, 106, 3497-3519 (2006)
[PDF]
Peptide Folding Simulations, S. Gnanakaran, H. Nymeyer,
J. Portman, K. Y. Sanbonmatsu and A. E. Garcia ,
Current Opinion in Structural Biology, 13, 168-174 (2003)
[PDF]
Atomic Simulations of Protein Folding, Using the Replica Exchange
Algorithm,
H. Nymeyer, S. Gnanakaran and A. E. Garcia,
Methods in Enzymology, 383, 119-149 (2004)
[PDF]
VALIDATE: A New Method for the Receptor-Based Prediction
of Binding Affinities of Novel Ligands, R. D. Head, M. L. Smythe,
T. I. Oprea, C. L. Waller, S. M. Green and G. R. Marshall,
Journal of the American Chemical Society, 118, 3959-3969 (1996)
[PDF]
The Protein Folding "Speed Limit", J. Kubelka, J. Hofrichter and
W. A. Eaton,
Current Opinion in Structural Biology, 14, 76-88 (2004)
[PDF]
De Novo Protein Design: Fully Automated Sequence Selection,
B. I. Dahiyat and S. L. Mayo,
Science, 278, 82-87 (1997)
[PDF]
Comprehensive and Quantitative Mapping of Energy Landscapes for
Protein-Protein Interactions by Rapid Combinatorial Scanning,
Gabor Pal, J.-L. K. Kouadio, D. R. Artis, A. A. Kossiakoff and S. S. Sidhu,
Journal of Biological Chemistry, 281, 22378-22385 (2006)
[PDF]
Chemometrics; What Do We Mean with It, and What Do We Want from It?,
S. Wold,
Chemometrics and Intelligent Laboratory Systems, 30,
109-115 (1995)
[PDF]
Introduction to Statistical Experimental Design, J. Trygg and S. Wold,
Chemometrics, Editorial, August 2002
[PDF]
Validated Ligand Mapping of ACE Active Site, D. J. Kuster and
G. R. Marshall
Journal of Computer-Aided Molecular Design, 19, 609-615 (2005)
[PDF]
What Affects mRNA Levels in Leaves of Field-Grown Aspen?
A Study of Developmental and Environmental Influences,
K. Wissel, F. Pettersson, A. Berglund and S. Jansson,
Plant Physiology, 133,1190-1197 (2003)
[PDF]
A Multivariate Approach Applied to Microarray Data for
Identification of Genes with Cell Cycle-Coupled Transcription,
D. Johansson, P. Lindgren and A. Berglund,
Bioinformatics, 19, 467-473 (2003)
[PDF]
The Equilibrium Unfolding of MerP Characterized
by Multivariate Analysis of 2D NMR Data,
A. Berglund, A.-C. Brorsson, B.-H. Jonsson and I. Sethson,
Journal of Magnetic Resonance, 172, 24-30 (2005)
[PDF]
Laboratory 1 (Sep 7): Minimization and Molecular Dynamics [TXT]
Laboratory 2 (Sep 14): Protein MD with Periodic Boundaries [TXT]
Laboratory 3 (Sep 21): Quantum Calculations with Gaussian 03 [TXT]
Laboratory 4 (Sep 28): Computing Properties of Liquids [TXT]
Laboratory 5 (Oct 12): Binding of Benzamidine to Trypsin [TXT]
Laboratory 6 (Oct 26): Homology Modeling - Part I [PDF]
Laboratory 7 (Nov 2): Homology Modeling - Part II [PDF]
Laboratory 8 (Nov 9): Sybyl and 3D QSAR - Part I [PDF]
Laboratory 9 (Nov 16): Sybyl and 3D QSAR - Part II [PDF]
Laboratory 10 (Nov 30): Ligand Refinement [PDF]
Laboratory 11 (Dec 7): Virtual Screening [PDF]