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VIPERdb specifications


Unique identifier OMICS_03086
Name VIPERdb
Alternative name Virus Particle Explorer database
Restrictions to use Academic or non-commercial use
Database management system MySQL
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes


  • CapsidMaps



  • person_outline Vijay S. Reddy

Publications for Virus Particle Explorer database

VIPERdb citations


A Rationally Engineered Capsid Variant of AAV9 for Systemic CNS Directed and Peripheral Tissue Detargeted Gene Delivery in Neonates

PMCID: 5948233
PMID: 29766031
DOI: 10.1016/j.omtm.2018.03.004
call_split See protocol

[…] d also to avoid steric hindrance when necessary. The model was not energy minimized. The coordinate of the VP3 trimer was generated for the CLv-D8 model and WT AAV9 crystal structure using the online VIPERdb server by icosahedral matrix multiplication. The CLv-D8 model was compared to the WT AAV9 structure, and potential losses/gains of interactions due to the residue mutations were analyzed inter […]


Influence of cell type and cell culture media on the propagation of foot and mouth disease virus with regard to vaccine quality

Virol J
PMCID: 5857075
PMID: 29548334
DOI: 10.1186/s12985-018-0956-0

[…] h the UCSF Chimera package []. Chimera was developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIGMS P41-GM103311). VIPERdb [] was used to extract contact information for specific residues. […]


Optimizing the Targeting of Mouse Parvovirus 1 to Murine Melanoma Selects for Recombinant Genomes and Novel Mutations in the Viral Capsid Gene

PMCID: 5850361
PMID: 29385689
DOI: 10.3390/v10020054
call_split See protocol

[…] rminal residue 47 to the last C-terminal residue, 587. This VP2 coordinate file was used to generate a 60-mer by T = 1 icosahedral matrix multiplication using the Oligomer Generator subroutine in the ViperDB online server ( [] to help visualize the location of the four variant residues, R54, S57, M70, and N348 in the MPV1p5-Bv1 variant compared to the […]


Atomic Resolution Structures of Human Bufaviruses Determined by Cryo Electron Microscopy

PMCID: 5795435
PMID: 29300333
DOI: 10.3390/v10010022

[…] ram was used to visualize the capsid surface morphology similarities and differences for the genus and subfamily level viruses compared. For this analysis, the capsid 60-mers were generated using the VIPERdb online server ( as described above []. […]


Atomic Resolution Structure of the Oncolytic Parvovirus LuIII by Electron Microscopy and 3D Image Reconstruction

PMCID: 5707528
PMID: 29084163
DOI: 10.3390/v9110321

[…] ID: 1z14) as a template [,,]. The VP2 monomer model was used to generate an all-atom 60mer using the online VIPERdb Oligomer Generator for a T = 1 capsid by icosahedral matrix multiplication ( []. The 60mer was docked into the cryo-reconstructed map using the “Fit-in-map” function in the Chimera program []. Prior to this fitting, the density map was converted from the P […]


Germline viral “fossils” guide in silico reconstruction of a mid Cenozoic era marsupial adeno associated virus

Sci Rep
PMCID: 4932596
PMID: 27377618
DOI: 10.1038/srep28965
call_split See protocol

[…] AAV4, and AAV8. To enable description of the assembled mAAV-EVE1 capsid, the VP3 monomer model was used to generate a 60mer by icosahedral matrix multiplication in the Viperdb online server ( The VP3 and 60mer coordinates were used to generate secondary structure and capsid surface images, respectively, using the PyMol program. […]


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VIPERdb institution(s)
Department of Molecular Biology, TPC-6 The Scripps Research Institute, La Jolla, CA, USA; Computational Visualization Center, University of Texas at Austin Austin, TX, USA
VIPERdb funding source(s)
VIPERdb is a training/service and dissemination component of the NIH Research Resource: Multiscale Modeling Tools for Structural Biology (MMTSB), which is fully funded by the National Center for Research Resources of the National Institutes of Health (RR12255).

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