Page 11 - GPD-1-1

Gene & Protein in Disease Bioinformatics study of PCNP

Information (NCBI) (https://www.ncbi.nlm.nih.gov/) Table 1. List of various bioinformatics tools employed in the
with accession reference NP_065090.1. To accomplish present study.
this study, we employed various bioinformatics tools and S. No. Database/tool Functions
software as listed in Table 1.
1. National Center for To retrieve amino acid
2.2. 3D structure prediction Biotechnology Information sequence of protein
(https://www.ncbi.nlm.nih.gov/)
PCNP has no reported structure in the protein data bank 2. Protein Data Bank (https://www. Structure of protein
(PDB) database (https://www.rcsb.org) . Therefore, rcsb.org)
[13]
to generate the 3D structure, both protein comparative 3. AlphaFold (https://alphafold.ebi. Protein structure
homology and sequence-based structure modeling ac.uk/) construction
approaches were utilized. We adopted four DeepMind 4. RoseTTAFold (https://boinc. Protein structure
learning tools that predict the protein structures, for bakerlab.org/rosetta/) construction
example, AlphaFold (https://alphafold.ebi.ac.uk/), 5. I-TASSER (Iterative Threading Protein structure
RoseTTAFold (https://boinc.bakerlab.org/rosetta/), Assembly Refinement; https:// construction
Iterative Threading Assembly Refinement (I-TASSER) zhanggroup.org/I-TASSER/)
(https://zhanggroup.org/I-TASSER/), and Robetta (https:// 6. Robetta (https://robetta.bakerlab. Protein structure
robetta.bakerlab.org/) [14-17] . AlphaFold and RoseTTAFold org/) construction
are new computational tools that use deep learning 7. UCSF Chimera software version Graphical inspection and
algorithms to generate protein structures. Besides, they 1.14 representation of the models
predict the protein structures in cases where no homology 8. SAVES meta-server version 6.0 To determine the quality
structure is known by incorporating the limited physical and (https://saves.mbi.ucla.edu/) factors of protein structure
biological knowledge into the deep learning algorithms [18,19] . 9. Quality Model Energy Analysis Quality of a protein
I-TASSER and Robetta are publicly available web-based (QMEAN; https://swissmodel. structure by deriving the
tools that predict 3D protein structure. They use the amino expasy.org/qmean/) local or global scores in
acid sequence as input and generate the 3D structure either terms of Z-score
by searching for multiple threading alignments for the 10. GROMACS software Molecular dynamic simulation
template from the PDB or using iterative structural assembly of protein structure
simulations, a de novo structure prediction method [16,17] . 11. ProtParam tool of ExPASy To determine the basic
Graphical inspection and representation of the models were (http://web.expasy.org/ physicochemical properties
protparam/)
done using UCSF Chimera software version 1.14 (http://
[20]
www.cgl.ucsf.edu/chimera/) . 12. SOPMA (https://npsa-prabi.ibcp. For the secondary structure
fr/cgi-bin/npsa_automat.pl?page=/ prediction of a protein
Furthermore, the resultant structures from the NPSA/npsa_sopma.html)
aforementioned tools were further subjected to the 13. GeneMANIA server (https:// To check the co-expression
ERRAT and PROCHECK tools. Both are in-built tools of genemania.org/) analysis of a protein
the Structure Analysis and Verification Server (SAVES) 14. STRING protein database PPI of protein
meta-server version 6.0 (https://saves.mbi.ucla.edu/) that (https://string-db.org/)
determine the quality factors (degree of appropriateness) 15. Cytoscape software version 3.8.2 To construct the coexpression
and stereochemical evaluation of the query protein and PPI networks
structure [21,22] . In addition, the quality model energy analysis 16. Network-Analyst server (https:// To assimilate the biological
(QMEAN) was performed using the QMEAN server www.networkanalyst.ca/) processes, molecular
accessed from https://swissmodel.expasy.org/qmean/. It is functions and cellular
components, and to enrich
a composite scoring function that estimates the quality of a pathway analysis of protein
protein structure model by deriving the local (per residue) 17. Enrichr web-server (https:// To validate the Network
or global (for the entire protein structure) scores in terms maayanlab.cloud/Enrichr/) Analyst results
of a Z-score . 18. Molecular Evolutionary Genetic To construct phylogenetic
[23]
Analysis (MEGA Home; tree of gene
2.3. Molecular dynamic simulation (MDS) megasoftware.net)
MDS of the best scored PCNP protein structure from the 19. Sequence Demarcation Tool For pairwise sequence
above-mentioned tools was carried out using GROMACS Version 1.2 (SDTv1.2; http://web. identity of a gene in
software . In in silico studies, MDS is considered the key cbio.uct.ac.za/~brejnev/) evolutionary analysis
[24]
analysis to identify the interactions of protein molecules and 20. Google Scholar To retrieve the literature
their structural characteristics . For MDS run, the PCNP PPI: Protein-protein interaction
[25]

Volume 1 Issue 1 (2022) 3 https://doi.org/10.36922/gpd.v1i1.65