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SPdb specifications


Unique identifier OMICS_05732
Name SPdb
Restrictions to use None
Maintained Yes


  • person_outline Shoba Rangathan

Publication for SPdb

SPdb citations


“In Silico” Characterization of 3 Phytase A and 3 Phytase B from Aspergillus niger

PMCID: 5733987
PMID: 29348934
DOI: 10.1155/2017/9746191

[…] between the ε-NH2 groups of the lysines and the side chains of Glutamate acid residues (E) and Aspartate (D) or basic residues of histidine (H), Arginine (R), and lysine (K) were performed using the SPDB-viewer 4.01 program [, ]. […]


Structural basis to stabilize the domain motion of BARD1 ARD BRCT by CstF50

Sci Rep
PMCID: 5478621
PMID: 28634376
DOI: 10.1038/s41598-017-03816-4

[…] h comprises 4, N-terminal ankyrin repeats containing α-helices, a linker, two BRCT repeats containing 3-α helices and three β- strands (Fig. ). BARD1 ARD-BRCT Gln 564 His mutation was generated using SPDB viewer. The BARD1 ARD-BRCT and Gln 564 His mutant structures were superimposed for direct comparison between wild-type and Mutant models (Fig. ). Modeled structure of CstF50 shows N-terminal heli […]


Purification and characterization of a novel cold adapted fungal glucoamylase

Microb Cell Fact
PMCID: 5414198
PMID: 28464820
DOI: 10.1186/s12934-017-0693-x

[…] osen for modeling, which is the crystal structure of Hypocrea jecorina glucoamylase (HjGa), which has 90% coverage and 69% identity with AmyT1. Distance calculations and models were created using the spdb viewer []. […]


A Novel Binding Mode Reveals Two Distinct Classes of NMDA Receptor GluN2B selective Antagonists

PMCID: 4859819
PMID: 26912815
DOI: 10.1124/mol.115.103036

[…] ucture. Gridspacing was 1.0 and padding 1.09. The volume that ifenprodil and EVT-101 occupy in the previously defined pocket was then calculated using the function "neighbors of selected residues" in SPDB Viewer (), with a 1.6 Å search radius around each compound. The "common pocket" volume was estimated by calculating the arithmetic mean between the volume occupied by ifenprodil in the EVT-101 ca […]


Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing

BMC Genomics
PMCID: 4769843
PMID: 26922242
DOI: 10.1186/s12864-016-2490-z

[…] c8956/geneCapture_all_rep_c10521 we used sequences obtained in the course of this work and deposited in the Pine Gene Capture database (PGC, http://www.scbi.uma.es/pgc/). Finally for P. pinaster AS4 [SPDB: sp_v3.0_unigene97582/sp_v3.0_unigene8248] we used the sequence obtained from our transcriptomic database SustainPineDB [] (http://www.scbi.uma.es/sustainpinedb/).The CLUSTALW program was used fo […]


In vitro cytotoxic and in silico activity of piperine isolated from Piper nigrum fruits Linn

PMCID: 4731375
PMID: 26820894
DOI: 10.1186/s40203-015-0013-2

[…] The three dimensional structure of target protein EGFR tyrosine kinase (PDB ID:2J5F) was downloaded from PDB (www.rcsb.org/pdb) structural database. This file was then opened in SPDB viewer edited by removing the heteroatoms, adding C terminal oxygen. The active pockets on target protein molecule were found out using CASTp server (Binkowski et al. ). The ligands were drawn us […]


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SPdb institution(s)
Department of Biochemistry, National University of Singapore, Singapore

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