Proteins conformational search

K Yue, KA Dill. Folding proteins with a simple energy function and extensive conformational searching. Protein Sci 5 254-261, 1996. 

Abagyan, R., Batalov, S., Cardozo, T., Totrov, M., Webber, J., and Zhou, Y. (1997) Homology modeling with internal coordinate mechanics deformation zone mapping and improvements of models via conformational search. Proteins Suppl 1, 29-37. 

A variety of theories for flexible macromolecules (rod, spheres, cylinders, etc.) have been proposed, many of them being geared toward the study of polymers and DNA (see Conformational Sampling Conformational Search Linear Chains Conformational Search Proteins and Polymers Structural Representation), A brief discussion of representative methodologies for polymers, proteins, and nucleic acids follows. 

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... 

Enzyme flexibility may influence the reaction in different ways (see Conformational Search Proteins and Molecular... 

Conformational Sampling Conformational Search Linear Chains Conformational Search Proteins Systematic and Random Search Methods for Finding Conformers of Molecules. 

Many of the techniques described previously for structure prediction of macromolecules and docking predictions can be applied to the conformation analysis of small molecules with a view to energy minimization or constraint satisfaction. (See Conformational Analysis 1 Conformational Analysis 2 Conformational Analysis 3 Conformational Search Linear Chains Conformational Search Medium-sized Molecules and Conformational Search Proteins.)... 

Conformational Sampling Conformational Search Proteins Distance Geometry Theory, Algorithms, and Chemical Applications Macromolecular Structures Determined using NMR Data NMR Refinement Simulated Anneeding. 

Comparative Molecular Field Analysis (CoMFA) Conformational Flexibility in 3D Structure Searching Conformational Search Medium-sized Molecules Conformational Search Proteins Genetic and Evolutionary Algorithms Molecular Docking and Structure-based Design Shape Analysis Structural Similarity Measures for Database Searching Structure and Substructure Searching Structure Databases. 

Conformational Search Proteins 1 562 University Politehnica of Bucharest, Romania... 

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