scholarly journals In silico functional dissection of saturation mutagenesis: Interpreting the relationship between phenotypes and changes in protein stability, interactions and activity

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Douglas E. V. Pires ◽  
Jing Chen ◽  
Tom L. Blundell ◽  
David B. Ascher
Keyword(s):  
Protein Stability ◽  
In Silico ◽  
Saturation Mutagenesis ◽  
The Relationship

scholarly journals In silico saturation mutagenesis of cancer genes

Nature ◽  
2021 ◽  
Author(s):  
Ferran Muiños ◽  
Francisco Martínez-Jiménez ◽  
Oriol Pich ◽  
Abel Gonzalez-Perez ◽  
Nuria Lopez-Bigas
Keyword(s):  
In Silico ◽  
Saturation Mutagenesis ◽  
Cancer Genes

scholarly journals Efficient In Silico Saturation Mutagenesis of a Member of the Caspase Protease Family

2021 ◽  
Author(s):  
Christoph Öhlknecht ◽  
Sonja Katz ◽  
Christina Kröß ◽  
Bernhard Sprenger ◽  
Petra Engele ◽  
...  
Keyword(s):  
In Silico ◽  
Saturation Mutagenesis

scholarly journals A computational in silico approach to predict high-risk coding and non-coding SNPs of human PLCG1 gene

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0260054
Author(s):  
Safayat Mahmud Khan ◽  
Ar-Rafi Md. Faisal ◽  
Tasnin Akter Nila ◽  
Nabila Nawar Binti ◽  
Md. Ismail Hosen ◽  
...  
Keyword(s):  
Protein Structure ◽  
T Cell ◽  
Protein Stability ◽  
In Silico ◽  
Catalytic Domain ◽  
Cell Lymphoma ◽  
Computational Study ◽  
Solvent Accessibility ◽  
T Cell Lymphoma ◽  
Post Translational Modification

PLCG1 gene is responsible for many T-cell lymphoma subtypes, including peripheral T-cell lymphoma (PTCL), angioimmunoblastic T-cell lymphoma (AITL), cutaneous T-cell lymphoma (CTCL), adult T-cell leukemia/lymphoma along with other diseases. Missense mutations of this gene have already been found in patients of CTCL and AITL. The non-synonymous single nucleotide polymorphisms (nsSNPs) can alter the protein structure as well as its functions. In this study, probable deleterious and disease-related nsSNPs in PLCG1 were identified using SIFT, PROVEAN, PolyPhen-2, PhD-SNP, Pmut, and SNPS&GO tools. Further, their effect on protein stability was checked along with conservation and solvent accessibility analysis by I-mutant 2.0, MUpro, Consurf, and Netsurf 2.0 server. Some SNPs were finalized for structural analysis with PyMol and BIOVIA discovery studio visualizer. Out of the 16 nsSNPs which were found to be deleterious, ten nsSNPs had an effect on protein stability, and six mutations (L411P, R355C, G493D, R1158H, A401V and L455F) were predicted to be highly conserved. Among the six highly conserved mutations, four nsSNPs (R355C, A401V, L411P and L455F) were part of the catalytic domain. L411P, L455F and G493D made significant structural change in the protein structure. Two mutations-Y210C and R1158H had post-translational modification. In the 5’ and 3’ untranslated region, three SNPs, rs139043247, rs543804707, and rs62621919 showed possible miRNA target sites and DNA binding sites. This in silico analysis has provided a structured dataset of PLCG1 gene for further in vivo researches. With the limitation of computational study, it can still prove to be an asset for the identification and treatment of multiple diseases associated with the target gene.

scholarly journals Class A β-lactamases and inhibitors: In silico analysis of the binding mode and the relationship with resistance

2018 ◽  
Vol 279 ◽  
pp. 37-46
Author(s):  
Rebeca Pereira ◽  
Vitor Won-Held Rabelo ◽  
Alexander Sibajev ◽  
Paula Alvarez Abreu ◽  
Helena Carla Castro
Keyword(s):  
In Silico ◽  
In Silico Analysis ◽  
Binding Mode ◽  
Class A ◽  
The Relationship ◽  
Silico Analysis

In silico saturation mutagenesis of cancer genes

2021 ◽  
Vol 53 (9) ◽  
pp. 1275-1275
Author(s):  
Ornob Alam
Keyword(s):  
In Silico ◽  
Saturation Mutagenesis ◽  
Cancer Genes
Sign in / Sign up

Export Citation Format

Share Document