Iterative Convex Quadratic Approximation for Global Optimization in Protein Docking
作者： Roummel F. Marcia , Julie C. Mitchell , J. Ben Rosen
DOI: 10.1007/S10589-005-4799-4
关键词: Regular polygon 、 Potential energy 、 Applied mathematics 、 Mathematics 、 Macromolecular docking 、 Maxima and minima 、 Mathematical optimization 、 Global optimization 、 Iterated function 、 Funnel 、 Quadratic equation
摘要: An algorithm for finding an approximate global minimum of a funnel shaped function with many local minima is described. It applied to compute the energy docking position ligand respect protein molecule. The method based on iterative use convex, general quadratic approximation that underestimates set minima, where error in minimized L1 norm. used generate reduced domain, which assumed contain function. Additional are computed this and improved computed. This process iterated until convergence tolerance satisfied. has been find generated by Docking Mesh Evaluator program. Results three different examples presented. Each these functions thousands minima. Convergence shown all examples.
springer.com
sci-hub.se 参考文章(12)
K. A. Dill, A. T. Phillips, J. B. Rosen, CGU: An Algorithm for Molecular Structure Prediction Large-Scale Optimization with Applications. ,vol. 94, pp. 1- 21 ,(1997) , 10.1007/978-1-4612-0693-4_1
J Ben Rosen, Haesun Park, John Glick, Lei Zhang, Accurate Solution to Overdetermined Linear Equations with Errors Using L1 Norm Minimization Computational Optimization and Applications. ,vol. 17, pp. 329- 341 ,(2000) , 10.1023/A:1026562601717
David S. Goodsell, Arthur J. Olson, Automated docking of substrates to proteins by simulated annealing. Proteins. ,vol. 8, pp. 195- 202 ,(1990) , 10.1002/PROT.340080302
J. Ben Rosen, Roummel F. Marcia, Convex Quadratic Approximation Computational Optimization and Applications. ,vol. 28, pp. 173- 184 ,(2004) , 10.1023/B:COAP.0000026883.13660.84
Jo�l Janin, Welcome to CAPRI: A Critical Assessment of PRedicted Interactions Proteins. ,vol. 47, pp. 257- 257 ,(2002) , 10.1002/PROT.10111
K.A. DILL, A.T. PHILLIPS, J.B. ROSEN, Protein structure and energy landscape dependence on sequence using a continuous energy function. Journal of Computational Biology. ,vol. 4, pp. 227- 239 ,(1997) , 10.1089/CMB.1997.4.227
Julie C. Mitchell, J. Ben Rosen, Andrew T. Phillips, Lynn F. Ten Eyck, Coupled optimization in protein docking research in computational molecular biology. pp. 280- 284 ,(1999) , 10.1145/299432.299502
Philip E. Gill, Walter Murray, Michael A. Saunders, Margaret H. Wright, User's Guide for NPSOL (Version 4.0): A Fortran Package for Nonlinear Programming. Defense Technical Information Center. ,(1986) , 10.21236/ADA169115
M. Holst, N. Baker, F. Wang, Adaptive multilevel finite element solution of the Poisson–Boltzmann equation I. Algorithms and examples Journal of Computational Chemistry. ,vol. 21, pp. 1319- 1342 ,(2000) , 10.1002/1096-987X(20001130)21:15<1319::AID-JCC1>3.0.CO;2-8
N. Baker, M. Holst, F. Wang, Adaptive multilevel finite element solution of the Poisson–Boltzmann equation II. Refinement at solvent‐accessible surfaces in biomolecular systems Journal of Computational Chemistry. ,vol. 21, pp. 1343- 1352 ,(2000) , 10.1002/1096-987X(20001130)21:15<1343::AID-JCC2>3.0.CO;2-K