The Static Modes: An alternative approach for the treatment of macro- and bio-molecular induced-fit flexibility

• Published in: The European physical journal. E, Soft matter and biological physics Vol. 28; no. 1; pp. 17 - 25
• Main Authors: Brut, M., Estève, A., Landa, G., Renvez, G., Djafari Rouhani, M.
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer-Verlag 01.01.2009; EDP Sciences; EDP Sciences: EPJ
• Subjects: Acrylic Resins - chemistry; Acrylic Resins - metabolism; Algorithms; Applied sciences; Biochemistry, Molecular Biology; Biological and Medical Physics; Biomechanics; Biophysics; Chemical Sciences; Complex Fluids and Microfluidics; Complex Systems; Deoxyadenine Nucleotides - chemistry; Deoxyadenine Nucleotides - metabolism; Exact sciences and technology; Hydrogen Bonding; Life Sciences; Macromolecular Substances - chemistry; Macromolecular Substances - metabolism; Mechanics; Models, Molecular; Molecular Conformation; Nanotechnology; or physical chemistry; Organic polymers; Physicochemistry of polymers; Physics; Physics and Astronomy; Polymer Sciences; Properties and characterization; Regular Article; Soft and Granular Matter; Structural Biology; Structure, morphology and analysis; Surfaces and Interfaces; Theoretical and; Thin Films; Thymidine Monophosphate - chemistry; Thymidine Monophosphate - metabolism; 87.15.A- Theory, modeling, and computer simulation; 87.15.-v Biomolecules: structure and physical properties; 33.15.Bh General molecular conformation and symmetry; stereochemistry; Theoretical study; Computing method; Acrylamide derivative polymer; Molecular dynamics method; Conformational transition

We present a new competitive method for the atomic scale treatment of macromolecular flexibility called Static Mode method. This method is based on the “induced-fit” concept, i.e. it maps the intrinsic deformations of a macromolecule subject to diverse external excitations. The algorithm makes it po...