Dynamics Techniques and Applications to Proteins

L. Pedersen, T. Darden, Molecular dynamics techniques and applications to proteins, in The Encyclopedia of Computational Chemistry, Vbl. 3,... 

Proteins can be modeled as beads on a string, where each bead represents an amino acid residue (see Conformational Search Proteins Molecular Dynamics Techniques and Applications to Proteins and Protein Modeling Folding... 

AMI AMBER A Program for Simulation of Biological and Organic Molecules CHARMM The Energy Function and Its Parameterization Combined Quantum Mechanics and Molecular Mechanics Approaches to Chemical and Biochemical Reactivity Density Functional Theory (DFT), Hartree-Fock (HF), and the Self-consistent Field Divide and Conquer for Semiempirical MO Methods Electrostatic Catalysis Force Fields A General Discussion Force Fields CFF GROMOS Force Field Hybrid Methods Hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) Methods Mixed Quantum-Classical Methods MNDO MNDO/d Molecular Dynamics Techniques and Applications to Proteins OPLS Force Fields Parameterization of Semiempirical MO Methods PM3 Protein Force Fields Quantum Mechanical/Molecular Mechanical (QM/MM) Coupled Potentials Quantum Mecha-nics/Molecular Mechanics (QM/MM) SINDOI Parameterization and Application. 

Aqueous Interfaces Biomembranes Modeling CHAR-MM The Energy Function and Its Parameterization Hydrophobic Effect Molecular Dynamics Studies of Lipid Bilayers Molecular Dynamics Techniques and Applications to Proteins Permeation of Lipid Membranes Molecular Dynamics Simulations Protein Force Fields. 

AMBER A Program for Simulation of Biological and Organic Molecules CHARMM The Energy Function and Its Parameterization Conformational Sanqfling Force Fields A Brief Introduction Force Fields A General Discussion Molecular Dynamics Techniques and Applications to Proteins OPLS Force Fields,... 

Usually refers to a method of solving Newton s equations of classical mechanics numerically, in order to propagate the positions and velocities of a system of molecules forward in time and thus to explore the phase space of the system. See Molecular Dynamics and Hybrid Monte Carlo in Systems with Multiple Time Scales and Long-range Forces Reference System Propagator Algorithms Molecular Dynamics DMA Molecular Dynamics Simulations of Nucleic Acids Molecular Dynamics Studies of Lipid Bilayers and Molecular Dynamics Techniques and Applications to Proteins. 

Molecular mechanics is broken down into several parts in this Encyclopedia. The qualitative aspects of the subject predate computational chemistry, and are to be found in Conformational Analysis 1 Conformational Analysis 2 and Conformational Analysis 3. A brief introduction to molecular mechanics itself is given in Force Fields A Brief Introduction. Molecular dynamics is discussed in many articles, including Molecular Dynamics Techniques and Applications to Proteins. Much of the remainder of molecular mechanics is concerned with, force fields and is summarized in Force Fields A General Discussion, or under the specific type of compound involved, e.g., carbohydrates (see Carbohydrate Force Fields) or nucleic acids (see Nucleic Acid Force Fields). 

Dynamics Simulations of Nucleic Acids). Recently, the most promising approach directed toward accurate treatment of the long range electrostatic effects seems to be the particle mesh Ewald (PME) method see Molecular Dynamics Techniques and Applications to Proteins). 

Free Energy Calculations Methods and Applications Free Energy Perturbation Calculations Free Energy Simulations Hydrogen Bonding 1 Hydrogen Bonding 2 Molecular Dynamics DNA Molecular Dynamics Simulations of Nucleic Acids Molecular Dynamics Techniques and Applications to Proteins Nucleic Acid Force Fields Poisson-Boltzmann Type Equations Numerical Methods Protein Force Fields. 

Lee Pedersen University of North Carolina, Chapel Hill, NC, USA Molecular Dynamics Techniques and Applications to Proteins 3 1650... 

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