3Drefine: an interactive web server for efficient protein structure refinement

By Debswapna Bhattacharya, Jackson Nowotny, Renzhi Cao, Jianlin Cheng. Nucleic Acids Res., 2016

377 citations recorded by the source corpus.

3Drefine is an interactive web server for consistent and computationally efficient protein structure refinement with the capability to perform web-based statistical and visual analysis. The 3Drefine refinement protocol utilizes iterative optimization of hydrogen bonding network combined with atomic-level energy minimization on the optimized model using a composite physics and knowledge-based force fields for efficient protein structure refinement. The method has been extensively evaluated on blind CASP experiments as well as on large-scale and diverse benchmark datasets and exhibits consistent improvement over the initial structure in both global and local structural quality measures. The 3Drefine web server allows for convenient protein structure refinement through a text or file input submission, email notification, provided example submission and is freely available without any registration requirement. The server also provides comprehensive analysis of submissions through various energy and statistical feedback and interactive visualization of multiple refined models through the JSmol applet that is equipped with numerous protein model analysis tools. The web server has been extensively tested and used by many users. As a result, the 3Drefine web server conveniently provides a useful tool easily accessible to the community. The 3Drefine web server has been made publicly available at the URL: http://sysbio.rnet.missouri.edu/3Drefine/.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b22c9995202f7e758300461d59b9b0b9aec26918

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

In Molecular Biology

Citations in the corpus

Computational protein structure refinement: Almost there, yet still so far to go (2017, background): “Although refinement web servers have become available, they tend to offer only a limited amount of refinement.(55,83,181,187) It will require additional efforts and resources to focus on optimizing computational efficiency for MD-based methods so that more significant refinement via web-based servic”
Protein tertiary structure modeling driven by deep learning and contact distance prediction in CASP13 (2019, methodology): “Otherwise, it was discarded and 3DRefine 49 was used to refine the top ranked model to generate a refined final model.”