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231226s2023 xx |||||o 00| ||eng c |
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|a 10.1002/jcc.27092
|2 doi
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|a pubmed24n1177.xml
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|a (DE-627)NLM35315993X
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|a (NLM)36809651
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|a DE-627
|b ger
|c DE-627
|e rakwb
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|a eng
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| 100 |
1 |
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|a Lee, Changsoo
|e verfasserin
|4 aut
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| 245 |
1 |
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|a GalaxyDock2-HEME
|b Protein-ligand docking for heme proteins
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| 264 |
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|c 2023
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|a Text
|b txt
|2 rdacontent
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|a ƒaComputermedien
|b c
|2 rdamedia
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|a ƒa Online-Ressource
|b cr
|2 rdacarrier
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|a Date Completed 25.04.2023
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|a Date Revised 13.06.2023
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|a published: Print-Electronic
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|a Citation Status MEDLINE
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|a © 2023 Wiley Periodicals LLC.
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|a Prediction of protein-ligand binding poses is an essential component for understanding protein-ligand interactions and computer-aided drug design. Various proteins involve prosthetic groups such as heme for their functions, and adequate consideration of the prosthetic groups is vital for protein-ligand docking. Here, we extend the GalaxyDock2 protein-ligand docking algorithm to handle ligand docking to heme proteins. Docking to heme proteins involves increased complexity because the interaction of heme iron and ligand has covalent nature. GalaxyDock2-HEME, a new protein-ligand docking program for heme proteins, has been developed based on GalaxyDock2 by adding an orientation-dependent scoring term to describe heme iron-ligand coordination interaction. This new docking program performs better than other noncommercial docking programs such as EADock with MMBP, AutoDock Vina, PLANTS, LeDock, and GalaxyDock2 on a heme protein-ligand docking benchmark set in which ligands are known to bind iron. In addition, docking results on two other sets of heme protein-ligand complexes in which ligands do not bind iron show that GalaxyDock2-HEME does not have a high bias toward iron binding compared to other docking programs. This implies that the new docking program can distinguish iron binders from noniron binders for heme proteins
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4 |
|a Journal Article
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4 |
|a Research Support, Non-U.S. Gov't
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| 650 |
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4 |
|a coordination bond potential
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| 650 |
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4 |
|a energy parameter optimization
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| 650 |
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4 |
|a heme proteins
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| 650 |
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4 |
|a protein-ligand docking
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| 650 |
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|a Hemeproteins
|2 NLM
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| 650 |
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7 |
|a Ligands
|2 NLM
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| 650 |
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7 |
|a Heme
|2 NLM
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| 650 |
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7 |
|a 42VZT0U6YR
|2 NLM
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| 700 |
1 |
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|a Yang, Jinsol
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Kwon, Sohee
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Seok, Chaok
|e verfasserin
|4 aut
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| 773 |
0 |
8 |
|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 44(2023), 14 vom: 30. Mai, Seite 1369-1380
|w (DE-627)NLM098138448
|x 1096-987X
|7 nnns
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| 773 |
1 |
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|g volume:44
|g year:2023
|g number:14
|g day:30
|g month:05
|g pages:1369-1380
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| 856 |
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|u http://dx.doi.org/10.1002/jcc.27092
|3 Volltext
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