Dill, K. A., Phillips, A. T. and Rosen, J. B. (1997), Protein structure and energy landscape dependence on sequence using a continuous energy function. J. Comp. Bio., 4(3): 227-239.  Home/Search   Document Details and Download   Summary   Related Articles   Check

....minima are major obstacles in search of the global minimum. Most deformation methods described up to now try to lower these energy barriers. A completely different way to deal with the problem is to approach the energy landscape from below. The CGU method, introduced by Dill, Phillips and Rosen [44] constructs a convex function that underestimates a set of known local minima. The main advantage is that the method is not affected by the heights of kinetic barriers. The CGU method is designed to fit all known local minima with a convex function which underestimates all of them, but which ....

....a basis of a new quadratic underestimation. The generality of the concept allows a variety of practical implementations; this quadratic CGU is probably the most simple one. The CGU method has been applied to peptides (up to 36 residues) using a simplified chain representation and energy function [44]. The method succeeded in finding the lowest energy structures. Moreover it was found to be largely independent of the amino acid sequence. This is a result of the fact that the underestimator doesn t look at the barriers of the energy landscape but explores the underside. Computer time scales as ....

K.A.Dill, A.T.Phillips, J.B.Rosen, Protein structure and energy landscape dependence on sequence using a continuous energy function, J.Comp.Biol. 4,3 (1997), 227 43

.... Science and Engineering San Diego Supercomputer Center University of California, San Diego University of California, San Diego jbrosen ucsd.edu teneyckl sdsc.edu Abstract Here, we introduce a new approach to macromolecular docking which combines the continuous global optimization algorithm CGU [6, 21] with the grid based conformational search engine DOT [23] We also detail the use of this method to dock acetylcholine into the fasciculin acetylcholinesterase complex. Fasciculin blocks access to the long, narrow pathway leading to the active site, which is located in the interior of the ....

.... algorithm along with a number of other discrete scanning methods [8, 13, 14, 16, 26, 27] The latter encompasses a wider variety of techniques, including molecular dynamics and statistical mechanics [3, 5, 11, 22] Monte Carlo and genetic algorithms [4, 19] underestimation or tunneling methods [6, 7, 21] such as CGU, and procedures for smoothing energy landscapes [15, 17, 20, 25] Instead of utilizing a single refinement technique, we have here coupled a discrete algorithm with a continuous one. While this idea was arrived at independently, it most certainly can be found in the work of others. We ....

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Dill, K. A., Phillips, A. T. and Rosen, J. B. (1997), Protein structure and energy landscape dependence on sequence using a continuous energy function. J. Comp. Bio., 4(3): 227-239.

....so it is impossible to study how global minima shift with changes in parameters. The technology that enables us to to beyond this limitation is the recently developed CGU (Convex Global Underestimator) method that is able to nd global minima of energy landscapes, at least for short enough chains [5, 6]. We describe here a new computational method that searches for globally optimal parameters for continuous models. It takes as input: 1) a given model and its associated adjustable parameters, 2) the incorrect best structure for each of m di erent molecules that is predicted by the starting ....

Dill, K.A., Phillips, A.T. & Rosen, J.B. (1997), \Protein structure and energy landscape dependence on sequence using a continuous energy function, " J. Comp. Bio. 4:227-239.

....Lynn F. TenEyck ComputerScienceandEngineering SanDiegoSupercomputerCenter University ofCalifornia,SanDiego University ofCalifornia,SanDiego jbrosen ucsd.edu teneyckl sdsc.edu Abstract Here,weintroducea new approach tomacromoleculardockingwhich combinesthecontinuousglobaloptimizationalgorithmCGU [6,22]withthegrid basedconformationalsearch engineDOT [24] W e alsodetailtheuseofthismethod todock acetylcholineintothefasciculin acetylcholinesterase complex.Fasciculinblo cksaccesstothelong,narrow pathway leadingtotheactivesite,which islocatedintheinterior ....

....z For informationon CGU, pleasevisitthe CGU home page at: http: cgu.cs.uw ec.edu. The latterencompassesawidervariety oftechniques,includingmoleculardynamicsand statisticalmechanics[3,11,16, 23] Mon teCarloand geneticalgorithms[4,20] underestimationor tunneling methods[6,7,22]such asCGU, and proceduresforsmoothingenergylandscapes[15,18,21,26] Insteadofutilizinga singlereflnement technique,we have herecoupleda discretealgorithmwitha continuousone. Whilethisideawasarrived atindependently,itmost certainlycanbe foundintheworkofothers.W e citeasjust oneexampletheAutoDock ....

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Dill,K. A.,Phillips,A. T. and Rosen,J.B. (1997), Proteinstructure and energy landscape dependence on sequence usinga continuousenergy function.J.Comp. Bio.,4(3):227-239.

....globaloptimization,we have developeda hybridor coupled optimizationtechniqueformoleculardocking.Coupledis synonymouswithunitedandjoined,which seemeda mostaptdescriptionofthisparticular method. Our approach combinestherapidscanningalgorithmDOT [21,34,35]withthe globaloptimizationtechniqueCGU [3, 27,30,28]. The two algorithmshave notbeen blended,butratherlinked ina cooperative scheme thatism utuallybeneflcial.Moreover, becauseCGU and DOT sharetheadvantageofbeingfullyparallelizable,thisuniflcation willprove increasinglyadvantageousintheageofteraopscomputing. 3 Rapid Scanningby Convolution The ....

.... needsofthebusinessworld acceleratedthedevelopmentoflinearprogrammingtechniques,andtheneedsofbioscience continue topushboundariesinnon convexoptimization.ConvexGlobalUnderestimation 7 (CGU) isan optimizationtechniquewhich arosefromcollaborationbetweenresearchersin computerscienceand biochemistry[3,27,30,28].AuthorsRosenand Phillipsdeveloped CGU alongwithKen Dill,and themethod hasbeensuccessfullytestedon a variety of proteinfoldingmo delswithup to70degreesoffreedom[3,27,30] Inadditiontoprotein foldinganddockingproblems,thealgorithmhasalsobeenusedtooptimizeparametersin ....

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Dill,K.A.,Phillips,A.T.andRosen,J.B.(1997),\Proteinstructureandenergylandscape dependenceon sequenceusinga continuousenergyfunction,"JournalofComputationalBiology, Vol.3,No.4.227-39.

....two roots of Eq (7) to define the new bounds of HOE. Another method would be simply to use HOE = fOE i : OE min ) i Gamma ffi i OE i (OE min ) i ffi i g where ffi i = j(OE min ) i Gamma (OE ) i j ; i = 1; n. For complete details of the CGU method and its computational results, see [5, 8]. ....

Dill, K.A., Phillips, A.T., and Rosen, J.B.: `Protein structure and energy landscape dependence on sequence using a continuous energy function', Journal of Computational Biology 4 (1997), 227-- 239.

....developed a hybrid or coupled optimization technique for molecular docking. Coupled is synonymous with united and joined, which seemed a most apt description of this particular method. Our approach combines the rapid scanning algorithm DOT [21, 35, 36] with the global optimization technique CGU [3, 27, 30, 28]. The two algorithms have not been blended, but rather linked in a cooperative scheme that is mutually beneficial. Moreover, because CGU and DOT share the advantage of being fully parallelizable, this unification will prove increasingly advantageous in the age of teraflops computing. 3 Rapid ....

....accelerated the development of linear programming techniques, and the needs of bioscience continue to push boundaries in non convex optimization. Convex Global Underestimation (CGU) is an optimization technique which arose from collaboration between researchers in computer science and biochemistry [3, 27, 30, 28]. Authors Rosen and Phillips developed CGU along with Ken Dill, and the method has been successfully tested on a variety of protein folding models with up to 70 degrees of freedom [3, 27, 30] In addition to protein folding and docking problems, the algorithm has also been used to optimize ....

[Article contains additional citation context not shown here]

Dill, K.A., Phillips, A.T. and Rosen, J.B. (1997), "Protein structure and energy landscape dependence on sequence using a continuous energy function," Journal of Computational Biology, Vol. 3, No. 4. 227-39.

....to improve the model. 3. The computer time required to find the native state is independent of monomer sequence, monomer composition, and native chain fold. The CGU search time doesn t depend on the shape of the landscape, and the CGU method does not get caught in kinetic traps. As shown in [9], the running time of the CGU algorithm is insensitive to the monomer sequence. For example, permutations of a 30 residue sequence (in which the percent hydrophobicity remained fixed across all cases) resulted in various model native structures. These computations also showed that the computation ....

....15 20 25 30 35 0.1 0.2 0.3 0.4 0.5 0.6 0.7 Figure 1.4 Energy Gap Between SA and CGU Figure 1. 5 True Native OE N (left) vs Model Native OE CGU (right) Structures for PPT position, i.e. sequence of hydrophobic (H) and polar (P) type residues, the CGU algorithm is also time invariant (see [9]) with respect to the specific monomer sequence, even though different sequences fold to very different model native structures. 4. The overall running times are quite reasonable at this stage: on a 32node Cray T3E, a 30 residue sequence requires one hour and a 50 residue sequence requires nine ....

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Dill, K.A., A.T. Phillips, and J.B. Rosen (1997), Protein structure and energy landscape dependence on sequence using a continuous energy function, Journal of Computational Biology 4(3):227-239.

....of real materials (with chemist John Weare, UCSD) and to particle methods. Ben Rosen, in conjunction with Ken Dill (Pharmaceutical Chemistry, UCSF) and Andy Phillips (CSci. USNA, and SDSC) are developing new parallel algorithms and software for computational biology applications [126][44]. An example is predicting molecular structure by computing the global minimum of the molecular energy function. Keith Marzullo is working on fault tolerance in the Nile project [95] 104] 96] an NSF National Challenge project initiated at Cornell to build a wide area execution environment for ....

K. A. Dill, J. B. Rosen and A.T.Phillips, "Protein Structure and Energy Landscape Dependence on Sequence using a Continuous Energy Function," Journal of Computational Biology 4, 1997, pp. 227-239.

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