Abstract
Why it is important to know this material?
Protein binding is implied in all biological mechanisms, and the definition of quantitative models and laws is essential to assess in a quantitative way the protein binding to small ligands, proteins, and nucleic acids.
What is the key idea?
Starting from molecular models, it is possible to determine the quantitative laws for protein binding.
What is necessary to know already?
It is essential to know how the protein structure is built and how it interacts with the environment, through a delicate interplay between stability and adaptability.
You take the blue pill…the story ends, you wake up in your bed and believe whatever you want to believe. You take the red pill…you stay in Wonderland, and I show you how deep the rabbit hole goes – Morpheus (The Matrix)
L. & L. Wachowski
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Notes
- 1.
The symplectic space refers to a vector space equipped with a symplectic form, which is a nondegenerate, closed, and skew-symmetric bilinear form. The symplectic form captures the geometric and algebraic structure of the space, providing a way to measure areas in phase space.
In simpler terms, a symplectic space is a mathematical framework used to study systems with continuous variables, such as position and momentum in physics. It allows for the analysis of the dynamics, stability, and conservation laws in these systems. Symplectic spaces have applications in various fields, including physics, mathematics, and computational biology, where they play a crucial role in understanding and modeling complex systems.
References
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Karplus M, Kuriyan J (2005) Proc Natl Acad Sci 102(19):6679–6685
Srivastava A et al (2018) Int J Mol Sci 19(11):3401
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Di Paola, L. (2024). Molecular Dynamics Simulations for Computational Biology. In: Fundamentals of Molecular Bioengineering. Springer, Cham. https://doi.org/10.1007/978-3-031-42022-1_8
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DOI: https://doi.org/10.1007/978-3-031-42022-1_8
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