In silico Tools at Early Stage of Pharmaceutical Development: Data Needs and Software Capabilities

2019 ◽  
Vol 20 (6) ◽  
Author(s):  
Juliet Obianuju Njoku ◽  
Daniela Amaral Silva ◽  
Dwaipayan Mukherjee ◽  
Gregory K. Webster ◽  
Raimar Löbenberg
Keyword(s):  
In Silico ◽  
Early Stage ◽  
Pharmaceutical Development ◽  
Development Data ◽  
In Silico Tools

Identification of BAP1-associated MicroRNAs and Implications in Cancer Development

2019 ◽  
pp. 1-4
Author(s):  
Tikam Chand ◽  
Tikam Chand
Keyword(s):  
Gene Regulation ◽  
In Silico ◽  
Mirna Target ◽  
Target Prediction ◽  
Differential Regulation ◽  
Cancer Development ◽  
Mirna Target Prediction ◽  
Cancer Types ◽  
In Silico Tools

Having role in gene regulation and silencing, miRNAs have been implicated in development and progression of a number of diseases, including cancer. Herein, I present potential miRNAs associated with BAP1 gene identified using in-silico tools such as TargetScan and Exiqon miRNA Target Prediction. I identified fifteen highly conserved miRNA (hsa-miR-423-5p, hsa-miR-3184-5p, hsa-miR-4319, hsa-miR125b-5p, hsa-miR-125a-5p, hsa-miR-6893-3p, hsa-miR-200b-3p, hsa-miR-200c-3p, hsa-miR-505-3p.1, hsa-miR-429, hsa-miR-370-3p, hsa-miR-125a-5p, hsa-miR-141-3p, hsa-miR-200a-3p, and hsa-miR-429) associated with BAP1 gene. We also predicted the differential regulation of these twelve miRNAs in different cancer types.

An Update of In Silico Tools for the Prediction of Pathogenesis in Missense Variants

2011 ◽  
Vol 6 (2) ◽  
pp. 185-198
Author(s):  
Alejandro j. Brea-Fernandez ◽  
Marta Ferro ◽  
Ceres Fernandez-Rozadilla ◽  
Ana Blanco ◽  
Laura Fachal ◽  
...  
Keyword(s):  
In Silico ◽  
Missense Variants ◽  
In Silico Tools

Deployment of in silico and in vitro safety assays in early-stage drug discovery

2012 ◽  
Vol 4 (10) ◽  
pp. 1211-1213 ◽  
Author(s):  
Yvonne Will ◽  
Thomas Schroeter
Keyword(s):  
Drug Discovery ◽  
In Silico ◽  
Early Stage

scholarly journals Antimicrobial peptide induced colloidal transformations in bacteria-mimetic vesicles: Combining in silico tools and experimental methods

2021 ◽  
Vol 596 ◽  
pp. 352-363
Author(s):  
Rafael V.M. Freire ◽  
Yeny Pillco-Valencia ◽  
Gabriel C.A. da Hora ◽  
Madeleine Ramstedt ◽  
Linda Sandblad ◽  
...  
Keyword(s):  
Antimicrobial Peptide ◽  
In Silico ◽  
Experimental Methods ◽  
In Silico Tools

scholarly journals A New Validation Methodology for In Silico Tools Based on X-ray Computed Tomography Images of Tablets and a Performance Analysis of One Tool

Pharmaceutics ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1488
Author(s):  
Sebastian Bollmann ◽  
Peter Kleinebudde
Keyword(s):  
Computed Tomography ◽  
In Silico ◽  
Pharmaceutical Formulations ◽  
Prediction Errors ◽  
Micro Computed Tomography ◽  
Pharmaceutical Dosage Forms ◽  
X Ray ◽  
Computed Tomography Images ◽  
X Ray Computed ◽  
In Silico Tools

In silico tools which predict the dissolution of pharmaceutical dosage forms using virtual matrices can be validated with virtual matrices based on X-ray micro-computed tomography images of real pharmaceutical formulations. Final processed images of 3 different tablet batches were used to check the performance of the in silico tool F-CAD. The goal of this work was to prove the performance of the software by comparing the predicted dissolution profiles to the experimental ones and to check the feasibility and application of the validation concept for in silico tools. Both virtual matrices based on X-ray micro-computed tomography images and designed by the software itself were used. The resulting dissolution curves were compared regarding their similarity to the experimental curve. The kinetics were analysed with the Higuchi and Korsmeyers–Peppas plot. The whole validation concept as such was feasible and worked well. It was possible to identify prediction errors of the software F-CAD and issues with the virtual tablets designed within the software.

scholarly journals Structure analysis of deleterious nsSNPs in human PALB2 protein for functional inference

2021 ◽  
Vol 17 (3) ◽  
pp. 424-438
Author(s):  
Noshin Nawar ◽  
Keyword(s):  
In Silico ◽  
General Outline ◽  
Recombination Repair ◽  
Functional Inference ◽  
Wd40 Domain ◽  
Project Data ◽  
Dbsnp Database ◽  
Comprehensive Characterization ◽  
In Silico Tools

Partner and Localizer of BRCA2 or PALB2 is a typical tumor suppressor protein, that responds to DNA double stranded breaks through homologous recombination repair. Heterozygous mutations in PALB2 are known to contribute to the susceptibility of breast and ovarian cancer. However, there is no comprehensive study characterizing the structural and functional impacts of SNPs located in the PALB2 gene.Therefore, it is of interest to document a comprehensive analysis of coding and non-coding SNPs located at the PALB2 loci using in silico tools. The data for 1455 non-synonymous SNPs (nsSNPs) located in the PALB2 loci were retrieved from the dbSNP database. Comprehensive characterization of the SNPs using a combination of in silico tools such as SIFT, PROVEAN, PolyPhen, PANTHER, PhDSNP, Pmut, MutPred 2.0 and SNAP-2, identified 28 functionally important SNPs. Among these, 16 nsSNPs were further selected for structural analysis using conservation profile and protein stability. The most deleterious nsSNPs were documented within the WD40 domain of PALB2. A general outline of the structural consequences of each variant was developed using the HOPE project data. These 16 mutant structures were further modelled using SWISS Model and three most damaging mutant models (rs78179744, rs180177123 and rs45525135) were identified. The non-coding SNPs in the 3’ UTR region of the PALB2 gene were analyzed for altered miRNA target sites. The comprehensive characterization of the coding and non-coding SNPs in the PALB2 locus has provided a list of damaging SNPs with potential disease association. Further validation through genetic association study will reveal their clinical significance.

Sign in / Sign up

Export Citation Format

Share Document