Improve Research Reproducibility A Bio-protocol resource
Concise Method
tooltip

Model evaluation and validation

HA Hina Ahsan
MA Muhammad Asghar
SM Shaukat Iqbal Malik
request Request a Protocol
ask Ask a question
Favorite

The Procheck tool confirmed the stereochemical correctness and overall structural geometry of the protein structure42. The Ramachandran plot statistics were used to assess the model's stability and validate the residues. In addition, the Ramachandran plot and Z-score analysis were performed on four high-resolution GCSF structures selected from the PDB database with PDB ID 5GW943. Normal mode analysis (NMA) was also carried out to comprehend the stability and flexibility of the docked model. The iMod technique was used to calculate the degree of stability. The elastic network model, deformability, eigenvalue, and covariance matrix were computed44.

Copyright and License information: The Author(s) ©2024
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

post Post a Question
0 Q&A