東華大學圖書館 |

語系: 繁體中文

說明(常見問題)

回圖書館首頁

手機版館藏查詢

登入

回首頁

切換: 標籤 | MARC模式 | ISBD

An integrated approach to protein-pr...

Chen, Rong.

FindBook

Google Book

Amazon

博客來

An integrated approach to protein-protein docking.

紀錄類型:	書目-電子資源 : Monograph/item
正題名/作者:	An integrated approach to protein-protein docking./
作者:	Chen, Rong.
面頁冊數:	139 p.
附註:	Source: Dissertation Abstracts International, Volume: 64-08, Section: B, page: 3926.
Contained By:	Dissertation Abstracts International64-08B.
標題:	Engineering, Biomedical. -
電子資源:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3101069

An integrated approach to protein-protein docking.
Chen, Rong.

An integrated approach to protein-protein docking. - 139 p.

Source: Dissertation Abstracts International, Volume: 64-08, Section: B, page: 3926.

Thesis (Ph.D.)--Boston University, 2004.

Structural genomics aims to determine the 3-dimensional (3D) structure of every protein in the cell, and high throughput techniques such as yeast-II-hybrid and protein microarrays will eventually identify nearly all protein-protein interactions. Considerable attention is paid currently to the computational methods of investigating these interactions. One such method is protein-protein docking, which predicts the 3D structure of a protein complex starting from the 3D structures of two interacting partners.Subjects--Topical Terms:

1017684
Engineering, Biomedical.

An integrated approach to protein-protein docking.
LDR:03304nmm 2200301 4500 001 1855260
005 20040624070204.5
008 130614s2004 eng d
035 $a (UnM)AAI3101069
035 $a AAI3101069
040 $a UnM $c UnM
100 1 $a Chen, Rong. $3 1917541
245 1 0 $a An integrated approach to protein-protein docking.
300 $a 139 p.
500 $a Source: Dissertation Abstracts International, Volume: 64-08, Section: B, page: 3926.
500 $a Major Professor: Zhiping Weng.
502 $a Thesis (Ph.D.)--Boston University, 2004.
520 $a Structural genomics aims to determine the 3-dimensional (3D) structure of every protein in the cell, and high throughput techniques such as yeast-II-hybrid and protein microarrays will eventually identify nearly all protein-protein interactions. Considerable attention is paid currently to the computational methods of investigating these interactions. One such method is protein-protein docking, which predicts the 3D structure of a protein complex starting from the 3D structures of two interacting partners.
520 $a This dissertation describes an integrated approach to protein-protein docking: an initial-stage docking program ZDOCK followed by a refinement-stage docking program RDOCK. ZDOCK treats the receptor and the ligand as rigid bodies and uses conformation-change-tolerant scoring functions to fully explore the 3 rotational and 3 translational degrees of freedom. The rotational space is searched explicitly and the translational space is searched using a Fast Fourier Transform (FFT) algorithm to speed up the process. Several scoring functions are investigated, including a novel pairwise shape complementarity (PSC) function, Atomic Contact Energy (ACE)-based desolvation energy, Interface Atomic Contact Energy (IFACE), and coulombic electrostatic energy. The top 2000 predictions from MOCK are then minimized in RDOCK using a three-stage energy-minimization scheme with a special treatment of ionic side chains. The minimized structures are then re-evaluated using a more sophisticated binding free energy, which combines the molecular mechanics software CHARMM with a statistical desolvation energy ACE.
520 $a To evaluate the performance of my software as well as other docking groups' software, a non-redundant docking benchmark has been built by collecting all protein complexes with both complex structure and at least one independently determined monomer structure available. When tested against the benchmark, my integrated approach identified a near-native structure (within 2.5Å from the experimental structure) as the top prediction for 37% of test cases, and within the top 4 predictions for 49% of test cases. Its superior performance has also been demonstrated in a community-wide protein docking blind test, CAPRI, where we successfully predicted the complex structures for 4 targets and had some success in 3 others. An automatic docking server has also been built to serve the docking community.
590 $a School code: 0017.
650 4 $a Engineering, Biomedical. $3 1017684
650 4 $a Computer Science. $3 626642
650 4 $a Biophysics, General. $3 1019105
690 $a 0541
690 $a 0984
690 $a 0786
710 2 0 $a Boston University. $3 1017454
773 0 $t Dissertation Abstracts International $g 64-08B.
790 1 0 $a Weng, Zhiping, $e advisor
790 $a 0017
791 $a Ph.D.
792 $a 2004
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3101069