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Frontiers of Computer Science

ISSN 2095-2228

ISSN 2095-2236(Online)

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Front. Comput. Sci.    2025, Vol. 19 Issue (3) : 193910    https://doi.org/10.1007/s11704-024-40577-6
Interdisciplinary
PDB-assistant: an integrated Web tool for analyzing and editing PDBs
Yukun ZHAO1, Changsen ZHOU1, Jianhong GAN1, Zhi-Xiong XIAO1, Jianbo LU2(), Xu MA2(), Yang CAO1()
1. Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China
2. National Human Genetic Resources Center, Beijing 100081, China
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Corresponding Author(s): Jianbo LU,Xu MA,Yang CAO   
Just Accepted Date: 19 August 2024   Issue Date: 30 September 2024
 Cite this article:   
Yukun ZHAO,Changsen ZHOU,Jianhong GAN, et al. PDB-assistant: an integrated Web tool for analyzing and editing PDBs[J]. Front. Comput. Sci., 2025, 19(3): 193910.
 URL:  
https://academic.hep.com.cn/fcs/EN/10.1007/s11704-024-40577-6
https://academic.hep.com.cn/fcs/EN/Y2025/V19/I3/193910
Fig.1  The Web interface of PDB-assistant. (a) Homepage overview; (b) the Web interface of StructureAlign; (c) the output interface of StructureAlign, including alignment details and an interactive molecular 3D viewer
Catagory Tool name Description
PDB-Analysis StructureAlign Superposing two proteins to evaluate their structural similarity with customized-region alignment
BreakCheck Checking whether the input protein PDB file has main chain breaks
PDB2FAS Extracting protein sequences from a PDB file
PDB-Editing AA-Mutate Replacing residues of a given protein with the customized residues
PE-Minimize Generating the energy minimized conformation of the given protein
PDB-Repair Fixing missing atoms or residues of the given input
PDB-Split Splitting a protein complex into individual chains
PDB-Assemble Assembling multiple subunits to complex by referring to the template structure
PDB-ReNumber Modifying the residue indexes of a PDB file
PDB-AddH Adding hydrogen atoms on a given protein (CHARMM22 defined hydrogen atoms)
Tab.1  List of all tools included in PDB-assistant
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