Computational Biochemistry
Computer Simulations as a New Tool for Scientific Research:
Selected Problems in Computational Biology:
- Protein Folding: Lectures 3 & 4
- Protein Aggregation: Lectures 5 & 6
- Recommended: Biochemistry 42, 3151 (2003)
- Recommended: Biochemistry 45, 498 (2006)
- Recommended: Nature 435, 773 (2005)
- Recommended: Proc. Natl. Acad. Sci USA 101, 711 (2004)
- Recommended: Proc. Natl. Acad. Sci. USA 102, 315 (2005)
- Recommended: Proc. Natl. Acad. Sci. USA 100, 330 (2003)
- Recommended: Science 300, 486 (2003)
- Recommended: Ann. Rev. Biomed. Eng. 4, 155 (2002)
- Recommended: Nature Structural Biology 9, 308 (2002)
- Recommended: Nature 410, 165 (2001)
- Recommended: The EMBO Journal 21, 5682 (2002)
- Recommended: Proceedings National Academy Sciences USA 99, 2754 (2002)
- Recommended: Proceedings National Academy Sciences USA 99, 2760 (2002)
- Recommended: Proceedings National Academy Sciences USA 97, 9907 (2000)
- Recommended: Structure 11, 295 (2003)
- Recommended: Proc. Natl. Acad. Sci. USA 101, 14760 (2004)
- Protein Chaperones: Lecture 7
- Protein Forced Unfolding: Lecture 8
- Protein Forced Unbinding: Lecture 9
- Recommended: J. Weisel, H. Shuman, R. Litvinov, CurrOpinStructBiol, 13, 227 (2003)
- Recommended: M. Schlierf, H. Li, J. Fernandez, PNAS, 101, 7299 (2004)
- Recommended: E. Evans, PNAS, 98, 3784 (2001)
- Recommended: L. M. Coussens, Z. Werb, Nature, 420, 860 (2002)
- Recommended: Y. J. Kim, L. Borgis, N. M. Varki, A. Varki, PNAS, 95, 9325 (1998)
- Recommended: B. T. Marshall et al, Nature, 423, 190, (2003)
- Recommended: G. Bell, Science, 200, 618 (1978)
- Recommended: R. Alon, D. Hammer, T. Springer, Nature, 374, 539 (1995)
- Recommended: V. Barsegov, D. Thirumalai, PNAS, 102, 1835 (2005)
- Recommended: D. Thirumalai, D. Klimov, CurrOpinStructBiol, 9, 197 (1999)
- Recommended: D. Klimov and D. Thirumalai PNAS, 97, 2544 (2000)
- Recommended: Kolinski, J. Skolnick, Polymer, 45, 511 (2004)
- Recommended: W. Sommers et al, Cell, 103, 467, (2000)
- Recommended: E. Evans, A. Leung, V. Heinrich & C. Zhu, PNAS, 101, 11281 (2004)
Protein architecture:
Foundations of Biomolecular Simulations
- Molecular Mechanics: Lecture 12
- Force Field: Lecture 13
- Recommended: J. Phys. Chem. B 2003, 107, 5064-5073 (nice comparison of different force fields)
- Non-bonded interactions: Lecture 14 and Lecture 15
Running Molecular Dynamics Simulations
Algorithms Used in Molecular Dynamics Simulations
- MD Integrators: Lecture 18
- Constraints in MD Simulations: Lecture 19
- Recommended: J. Comp. Phys. 23, 327 (1977)
- Statistical Ensembles in MD Simulations: Lecture 20
- Multistep Integrators: Lecture 21
- Langevin Dynamics: Lecture 22
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