Chapter 5 - Energy minimization by smoothing techniques: a survey

[1]  M J Sippl,et al.  Cayley-Menger coordinates. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[2]  H. Verschelde,et al.  Calculating free energies of Lennard-Jones clusters using the effective diffused potential , 1998 .

[3]  C DeLisi,et al.  Multiple copy sampling in protein loop modeling: Computational efficiency and sensitivity to dihedral angle perturbations , 1994, Protein science : a publication of the Protein Society.

[4]  Ron Elber,et al.  The thermal equilibrium aspects of the time dependent Hartree and the locally enhanced sampling approximations: Formal properties, a correction, and computational examples for rare gas clusters , 1993 .

[5]  Lucjan Piela,et al.  Mean field theory as a tool for intramolecular conformational optimization. II: Tests on the homopolypeptides decaglycine and icosalanine , 1993 .

[6]  H. Scheraga,et al.  Application of the diffusion equation method for global optimization to oligopeptides , 1992 .

[7]  R. Somorjai,et al.  Applicability of the method of smoothed functionals as a global minimizer for model polypeptides , 1992 .

[8]  Frank H. Stillinger,et al.  Cluster optimization simplified by interaction modification , 1990 .

[9]  L. Piela,et al.  Mean field theory as a tool for intramolecular conformational optimization. 1. Tests on terminally-blocked alanine and met-enkephalin , 1992 .

[10]  M. Karplus,et al.  Multiple copy simultaneous search and construction of ligands in binding sites: application to inhibitors of HIV-1 aspartic proteinase. , 1993, Journal of medicinal chemistry.

[11]  Sigurd Schelstraete,et al.  Finding Minimum-Energy Configurations of Lennard-Jones Clusters Using an Effective Potential , 1997 .

[12]  Andrew E. Torda,et al.  Structure optimization combining soft-core interaction functions, the diffusion equation method, and molecular dynamics , 1997 .

[13]  M. Karplus,et al.  Enhanced sampling in molecular dynamics: use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin , 1990 .

[14]  J. Ben Rosen,et al.  Protein Structure and Energy Landscape Dependence on Sequence Using a Continuous Energy Function , 1997, J. Comput. Biol..

[15]  John E. Straub,et al.  Finding the needle in the haystack: algorithms for conformational optimization , 1996 .

[16]  H A Scheraga,et al.  Theoretical prediction of a crystal structure. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[17]  H. Scheraga,et al.  Performance of the diffusion equation method in searches for optimum structures of clusters of Lennard-Jones atoms , 1991 .

[18]  C. DeLisi,et al.  Computing the structure of bound peptides. Application to antigen recognition by class I major histocompatibility complex receptors. , 1993, Journal of molecular biology.

[19]  H. Scheraga,et al.  Solution of the embedding problem and decomposition of symmetric matrices. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[20]  Timothy F. Havel,et al.  The theory and practice of distance geometry , 1983, Bulletin of Mathematical Biology.

[21]  J. Straub,et al.  Simulation study of the collapse of linear and ring homopolymers , 1995 .

[22]  M. Karplus,et al.  Functionality maps of binding sites: A multiple copy simultaneous search method , 1991, Proteins.

[23]  R. Elber,et al.  Modeling side chains in peptides and proteins: Application of the locally enhanced sampling and the simulated annealing methods to find minimum energy conformations , 1991 .

[24]  An effective potential for calculating free energies. I. General concepts and approximations , 1997 .

[25]  J. Szulmajster.  Protein folding , 1988, Bioscience reports.

[26]  J. Doye,et al.  The effect of the range of the potential on the structures of clusters , 1995 .

[27]  J. Onuchic,et al.  Funnels, pathways, and the energy landscape of protein folding: A synthesis , 1994, Proteins.

[28]  Lucjan Piela,et al.  Performance of the shift method of global minimization in searches for optimum structures of clusters of Lennard-Jones atoms , 1992 .

[29]  L. Piela,et al.  Molecular Dynamics on Deformed Potential Energy Hypersurfaces , 1995 .

[30]  Jianpeng Ma,et al.  Simulated annealing using coarse grained classical dynamics: Smoluchowski dynamics in the Gaussian density approximation , 1995 .

[31]  Lucjan Piela,et al.  Smoothing techniques of global optimization: Distance scaling method in searches for most stable Lennard–Jones atomic clusters , 1997 .

[32]  H. Scheraga,et al.  On the multiple-minima problem in the conformational analysis of molecules: deformation of the potential energy hypersurface by the diffusion equation method , 1989 .

[33]  H. A. Scheraga,et al.  Application of the diffusion equation method of global optimization to water clusters , 1992 .

[34]  John E. Straub,et al.  FOLDING MODEL PROTEINS USING KINETIC AND THERMODYNAMIC ANNEALING OF THE CLASSICAL DENSITY DISTRIBUTION , 1995 .

[35]  F. Stillinger,et al.  Nonlinear optimization simplified by hypersurface deformation , 1988 .

[36]  C. Brooks,et al.  Cluster structure determination using Gaussian density distribution global minimization methods , 1994 .

[37]  J. Straub,et al.  Global energy minimum searches using an approximate solution of the imaginary time Schroedinger equation , 1993 .

[38]  Stillinger.  Role of potential-energy scaling in the low-temperature relaxation behavior of amorphous materials. , 1985, Physical review. B, Condensed matter.

[39]  R. Elber,et al.  Computational studies of ligand diffusion in globins: I. Leghemoglobin , 1991, Proteins.

[40]  Leonard M. Blumenthal,et al.  Theory and applications of distance geometry , 1954 .

[41]  Global optimization using ab initio quantum mechanical potentials and simulated annealing of the classical Liouville equation , 1995 .

[42]  John E. Straub.  OPTIMIZATION TECHNIQUES WITH APPLICATIONS TO PROTEINS , 1996 .

[43]  M. Orešič,et al.  Hierarchical characterization of energy landscapes using Gaussian packet states , 1994 .

[44]  G. M. Crippen,et al.  Why energy embedding works , 1987 .

[45]  Lucjan Piela,et al.  Mean field theory as a tool for intramolecular conformational optimization. 3. Test on melittin , 1993 .

[46]  Straub,et al.  Energy minimization using the classical density distribution: Application to sodium chloride clusters. , 1996, Physical review. B, Condensed matter.

[47]  H A Scheraga,et al.  An approach to the multiple-minima problem in protein folding by relaxing dimensionality. Tests on enkephalin. , 1987, Journal of molecular biology.

[48]  R. Somorjai.  Novel approach for computing the global minimum of proteins. 1. General concepts, methods, and approximations , 1991 .

[49]  Gordon M. Crippen,et al.  Conformational analysis by scaled energy embedding , 1984 .

[50]  Shugo Nakamura,et al.  CONFORMATIONAL ENERGY MINIMIZATION USING A TWO-STAGE METHOD , 1995 .

[51]  Gordon M. Crippen,et al.  Conformational analysis by energy embedding , 1982 .

[52]  Ron Elber,et al.  HYDROPHOBIC COLLAPSE IN A CYCLIC HEXAPEPTIDE : COMPUTER SIMULATIONS OF CHDLFC AND CAAAAC IN WATER , 1994 .

[53]  Wieslaw Nowak,et al.  Locally enhanced sampling in free energy calculations: Application of mean field approximation to accurate calculation of free energy differences , 1992 .

[54]  David Shalloway,et al.  Application of the renormalization group to deterministic global minimization of molecular conformation energy functions , 1992, J. Glob. Optim..

[55]  J. Straub,et al.  Approximate solution of the classical Liouville equation using Gaussian phase packet dynamics: Application to enhanced equilibrium averaging and global optimization , 1993 .

[56]  John E. Straub,et al.  ENERGY EQUIPARTITIONING IN THE CLASSICAL TIME-DEPENDENT HARTREE APPROXIMATION , 1991 .

[57]  Jianpeng Ma,et al.  Simulated annealing using the classical density distribution , 1994 .

[58]  J. Doll,et al.  Quantum annealing: A new method for minimizing multidimensional functions , 1994, chem-ph/9404003.

[59]  R. L. Somorjai,et al.  Novel approach for computing the global minimum of proteins. 2. One-dimensional test cases , 1991 .