Detailed Information on Publication Record
2008
In silico mutagenesis and docking studies of Pseudomonas aeruginosa lectin PA-IIL - predicting binding modes and energies
ADAM, Jan, Zdeněk KŘÍŽ, Martin PROKOP, Michaela WIMMEROVÁ, Jaroslav KOČA et. al.Basic information
Original name
In silico mutagenesis and docking studies of Pseudomonas aeruginosa lectin PA-IIL - predicting binding modes and energies
Name in Czech
In silico mutagenesis and docking studies of Pseudomonas aeruginosa lectin PA-IIL - predicting binding modes and energies
Authors
ADAM, Jan (203 Czech Republic), Zdeněk KŘÍŽ (203 Czech Republic), Martin PROKOP (203 Czech Republic), Michaela WIMMEROVÁ (203 Czech Republic) and Jaroslav KOČA (203 Czech Republic, guarantor)
Edition
Journal of Chemical Information and Modeling, 2008, 1549-9596
Other information
Language
English
Type of outcome
Článek v odborném periodiku
Field of Study
10600 1.6 Biological sciences
Country of publisher
Czech Republic
Confidentiality degree
není předmětem státního či obchodního tajemství
Impact factor
Impact factor: 3.643
RIV identification code
RIV/00216224:14310/08:00024957
Organization unit
Faculty of Science
UT WoS
000261103700013
Keywords in English
lectins; molecular modeling; computational chemistry; in silico prediction; docking
Tags
International impact, Reviewed
Změněno: 24/6/2009 12:53, prof. RNDr. Michaela Wimmerová, Ph.D.
V originále
This article is focused on the application of two types of AutoDock and DOCK docking software, and aimed at studying the interaction of a calcium-dependent bacterial lectin PA-IIL from Pseudomonas aeruginosa as well as its mutants with saccharide ligands. The effect of different partial charges assigned to the calcium ions was tested and evaluated in terms of the best agreement with the crystal structure. The results of DOCK were further optimized by molecular dynamics and rescored using AMBER. For both software, the agreement of the docked structures and the provided binding energies were evaluated in terms of prediction accuracy. This was carried out by comparing the computed results to the crystal structures and experimentally determined binding energies, respectively. The performance of the both docking software applied on studied problem was evaluated as well. The molecular docking methods proved efficient in identifying the correct binding modes in terms of geometry, and partially also in predicting the preference changes caused by mutation. Obtaining a reasonable in silico method for the prediction of lectin-saccharide interactions may be possible in the future.
In Czech
This article is focused on the application of two types of AutoDock and DOCK docking software, and aimed at studying the interaction of a calcium-dependent bacterial lectin PA-IIL from Pseudomonas aeruginosa as well as its mutants with saccharide ligands. The effect of different partial charges assigned to the calcium ions was tested and evaluated in terms of the best agreement with the crystal structure. The results of DOCK were further optimized by molecular dynamics and rescored using AMBER. For both software, the agreement of the docked structures and the provided binding energies were evaluated in terms of prediction accuracy. This was carried out by comparing the computed results to the crystal structures and experimentally determined binding energies, respectively. The performance of the both docking software applied on studied problem was evaluated as well. The molecular docking methods proved efficient in identifying the correct binding modes in terms of geometry, and partially also in predicting the preference changes caused by mutation. Obtaining a reasonable in silico method for the prediction of lectin-saccharide interactions may be possible in the future.
Links
| GA303/06/0570, research and development project |
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| LC06030, research and development project |
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| MSM0021622413, plan (intention) |
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