In molecular mechanics, current generation potential energy functions provide a reasonably good compromise between accuracy and effectiveness. This paper firstly reviewed several most commonly used classical potential energy functions and their optimization methods used for energy minimization. To minimize a potential energy function, about 95 \% efforts are spent on the Lennard-Jones potential of van der Waals interactions; we also give a detailed review on some effective computational optimization methods listed in the Cambridge Cluster Database to solve the problem of Lennard-Jones clusters. From the reviews, we found the hybrid idea of optimization methods is effective, necessary and efficient for solving the potential energy minimization problem and the Lennard-Jones clusters problem. An application to prion protein structures is then done by the hybrid idea; interesting results (e.g. (i) the species that has the clearly and highly ordered S2-H2 loop usually owns a 3-10-helix in this loop, (ii) a "pi-circle" Y128-F175-Y218-Y163-F175-Y169-R164-Y128(-Y162) is around the S2-H2 loop of prion protein structures) were found. \\%DIF > efforts are spent on the Lennard-Jones potential of van der Waals interactions; we also give a detailed review on some effective computational optimization methods in the Cambridge Cluster Database to solve the problem of Lennard-Jones clusters. From the reviews, we found the hybrid idea of optimization methods is effective, necessary and efficient for solving the potential energy minimization problem and the Lennard-Jones clusters problem. An application to prion protein structures is then done by the hybrid idea. We focus on the \beta2-\alpha2 loop of prion protein structures, and we found (i) the species that has the clearly and highly ordered \beta2-\alpha2 loop usually owns a 3_{10}-helix in this loop, (ii) a "\pi-circle" Y128--F175--Y218--Y163--F175--Y169--R164--Y128(--Y162) is around the \beta2-\alpha2 loop.
In molecular mechanics, current generation potential energy functions provide a reasonably good compromise between accuracy and effectiveness. This paper firstly reviewed several most commonly used classical potential energy functions and their optimization methods used for energy minimization. To minimize a potential energy function, about 95 \\%DIF > efforts are spent on the Lennard-Jones potential of van der Waals interactions; we also give a detailed review on some effective computational optimization methods in the Cambridge Cluster Database to solve the problem of Lennard-Jones clusters. From the reviews, we found the hybrid idea of optimization methods is effective, necessary and efficient for solving the potential energy minimization problem and the Lennard-Jones clusters problem. An application to prion protein structures is then done by the hybrid idea. We focus on the \beta2-\alpha2 loop of prion protein structures, and we found (i) the species that has the clearly and highly ordered \beta2-\alpha2 loop usually owns a 3_{10}-helix in this loop, (ii) a "\pi-circle" Y128--F175--Y218--Y163--F175--Y169--R164--Y128(--Y162) is around the \beta2-\alpha2 loop.
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\% efforts are spent on the Lennard-Jones potential of van der Waals interactions; we also give a detailed review on some effective computational optimization methods listed in the Cambridge Cluster Database to solve the problem of Lennard-Jones clusters. From the reviews, we found the hybrid idea of optimization methods is effective, necessary and efficient for solving the potential energy minimization problem and the Lennard-Jones clusters problem. An application to prion protein structures is then done by the hybrid idea; interesting results (e.g. (i) the species that has the clearly and highly ordered S2-H2 loop usually owns a 3-10-helix in this loop, (ii) a "pi-circle" Y128-F175-Y218-Y163-F175-Y169-R164-Y128(-Y162) is around the S2-H2 loop of prion protein structures) were found.