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Simple models of protein and small m...

Brem, Rachel Beth.

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Simple models of protein and small molecule systems.

紀錄類型:	書目-電子資源 : Monograph/item
正題名/作者:	Simple models of protein and small molecule systems./
作者:	Brem, Rachel Beth.
面頁冊數:	125 p.
附註:	Source: Dissertation Abstracts International, Volume: 61-11, Section: B, page: 5752.
Contained By:	Dissertation Abstracts International61-11B.
標題:	Biophysics, General. -
電子資源:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=9996544
ISBN:	0493038515

Simple models of protein and small molecule systems.
Brem, Rachel Beth.

Simple models of protein and small molecule systems. - 125 p.

Source: Dissertation Abstracts International, Volume: 61-11, Section: B, page: 5752.

Thesis (Ph.D.)--University of California, San Francisco, 2000.

This thesis uses simple models to address several questions in protein biophysics and liquid theory.

ISBN: 0493038515Subjects--Topical Terms:

1019105
Biophysics, General.

Simple models of protein and small molecule systems.
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245 1 0 $a Simple models of protein and small molecule systems.
300 $a 125 p.
500 $a Source: Dissertation Abstracts International, Volume: 61-11, Section: B, page: 5752.
500 $a Chair: Ken A. Dill.
502 $a Thesis (Ph.D.)--University of California, San Francisco, 2000.
520 $a This thesis uses simple models to address several questions in protein biophysics and liquid theory.
520 $a The work of the first chapter finds protein sequences of hydrophobic (H) and polar (P) residues that fold to a given target. We search H-P sequence space with a genetic algorithm, rewarding H-H contacts and penalizing exposed H's. In a lattice model, &sim;70% of designed sequences fold uniquely to their target. In biological proteins, designed and native sequences agree in &sim;70% of residue positions.
520 $a In the second chapter we ask, how severe are errors in protein-ligand scoring functions which disregard non-native ligand binding modes? We design such functions in a 2D lattice model of ligand binding, then train them against a "training set" of ligands. Errors in fitted parameters and free energies predicted by the scoring functions are as high as 25%. But if all ligands occupy the ground-state binding mode more than 50% of the time, errors are only &sim;10%.
520 $a The thesis's third chapter proposes a new way to estimate gamma, the strength of the hydrophobic effect, from oil-water partitioning data. Our protocol harnesses oil-phase enthalpies via the van Laar model. In lattice tests, van Laar theory recoups model oil-phase energy parameters to within 14%. The van Laar expression fits experimental enthalpies well ( r ≥ 0.9); the resulting estimate for gamma is &sim;40 cal/(mol A²).
520 $a We address in the fourth chapter the conventional wisdom that Flory-Huggins (FH) theory should not be used on sphere-like molecules. We find evidence against this hypothesis: FH predicts trends in cyclic, branched, and linear alkanes, in the iodine solvation data of Hildebrand, and in disk models of liquids.
520 $a In the fifth chapter we study the physical basis for the success of mole-fraction theory (MF) in Hildebrand's iodine solvation entropies. We re-formulate MF in terms of excess quantities; within &sim;15%, this version of MF agrees with entropies of experimental liquids, Monte-Carlo-simulated hard disks, and scaled particle theory. Results suggest that MF may describe the solution structure of sphere-like molecules.
590 $a School code: 0034.
650 4 $a Biophysics, General. $3 1019105
650 4 $a Biology, Molecular. $3 1017719
650 4 $a Chemistry, Physical. $3 560527
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690 $a 0494
710 2 0 $a University of California, San Francisco. $3 1025118
773 0 $t Dissertation Abstracts International $g 61-11B.
790 1 0 $a Dill, Ken A., $e advisor
790 $a 0034
791 $a Ph.D.
792 $a 2000
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