Earticle

초록

영어

Since it is of great importance to know how a ligand binds to a receptor, there have been a lot of efforts to improve the quality of prediction of docking poses. Earlier efforts were focused on improving search algorithm and scoring function in a docking program resulting in a partial improvement with a lot of variations. Although these are basically very important and essential, more tangible improvements came from the reduction of search space. In a normal docking study, the approximate active site is assumed to be known. After defining active site, scoring functions and search algorithms are used to locate the expected binding pose within this search space. A good search algorithm will sample wisely toward the correct binding pose. By careful study of receptor structure, it was possible to prioritize sub-space in the active site using “receptor-based pharmacophores”or “hot spots”. In a sense, these techniques reduce the search space from the beginning. Further improvements were made when the bound ligand structure is available, i.e., the searching could be directed by molecular similarity using ligand information. This could be very helpful to increase the accuracy of binding pose. In addition, if the biological activity data is available, docking program could be improved to the level of being useful in affinity prediction for a series of congeneric ligands. Since the number of co-crystal structures is increasing in protein databank, “Ligand-Guided Docking”to reduce the search space would be more important to improve the accuracy of docking pose prediction and the efficiency of virtual screening. Further improvements in this area would be useful to produce more reliable docking programs.

목차

Abstract
 1. 일반적인 도킹 프로그램 개발 상황
 2. 알고리듬을 통한 탐색공간의 축소
 3. 수용체의 구조정보를 이용하여 탐색공간을 축소하는 방법
  3.1. Cerius의 SBF
  3.2. GRID
 4. 결합하고 있는 리간드의 정보를 활용하여 탐색공간을 축소하는 방법 (“Ligand-Guided Docking”) 수용체의 구조정보를 이용하여 탐색공간을 축소하는 방법
  4.1. SG-Dock(Similarity-Guided Dock)과 SP-Dock(Similarity-Penalized Dock)1 Cerius의 SBF
  4.2. DOCKER
  4.3. AFMoC.2 DOCKER
 5. 탐색공간 축소 연구의 개발 방향
 참고문헌

키워드

저자

• 조승주 [ Seung Joo Cho | 조선대학교 의과대학 ] Corresponding author

참고문헌

발행기관

간행물

표지보기 관심저널 등록

• 간행물명

  통합자연과학논문집(구 조선자연과학논문집) [Journal of Integrative Natural Science]

• 간기

  계간

• pISSN

  2005-1042

• 수록기간

  2008~2025

• 등재여부

  KCI 등재

• 십진분류

  KDC 405 DDC 505