scholarly journals A three‐dimensional potential of mean force to improve backbone and sidechain hydrogen bond geometry in Xplor‐NIH protein structure determination

2019 ◽  
Vol 29 (1) ◽  
pp. 100-110 ◽  
Author(s):  
Charles D. Schwieters ◽  
Guillermo A. Bermejo ◽  
G. Marius Clore
Keyword(s):  
Hydrogen Bond ◽  
Protein Structure ◽  
Structure Determination ◽  
Three Dimensional ◽  
Protein Structure Determination ◽  
Potential Of Mean Force

scholarly journals Analytical tools in protein structure determination

2021 ◽  
Vol 8 (3) ◽  
pp. 103-111
Author(s):  
Krishna R Gupta ◽  
Uttam Patle ◽  
Uma Kabra ◽  
P. Mishra ◽  
Milind J Umekar
Keyword(s):  
Protein Structure ◽  
Structure Determination ◽  
Structure Prediction ◽  
Protein Structures ◽  
Three Dimensional ◽  
Protein Structure Determination ◽  
Computational Techniques ◽  
Determination Process ◽  
Structure Databases ◽  
Analytical Tools

Three-dimensional protein structure prediction from amino acid sequence has been a thought-provoking task for decades, but it of pivotal importance as it provides a better understanding of its function. In recent years, the methods for prediction of protein structures have advanced considerably. Computational techniques and increase in protein sequence and structure databases have influence the laborious protein structure determination process. Still there is no single method which can predict all the protein structures. In this review, we describe the four stages of protein structure determination. We have also explored the currenttechniques used to uncover the protein structure and highpoint best suitable method for a given protein.

scholarly journals PROBABILISTIC ENSEMBLES FOR IMPROVED INFERENCE IN PROTEIN-STRUCTURE DETERMINATION

2012 ◽  
Vol 10 (01) ◽  
pp. 1240009 ◽  
Author(s):  
AMEET SONI ◽  
JUDE SHAVLIK
Keyword(s):  
Protein Structure ◽  
Structure Determination ◽  
Protein Structures ◽  
Three Dimensional ◽  
Protein Structure Determination ◽  
Complex Problem ◽  
Approximate Inference ◽  
X Ray ◽  
X Ray Crystallography ◽  
Inference Methods

Protein X-ray crystallography — the most popular method for determining protein structures — remains a laborious process requiring a great deal of manual crystallographer effort to interpret low-quality protein images. Automating this process is critical in creating a high-throughput protein-structure determination pipeline. Previously, our group developed ACMI, a probabilistic framework for producing protein-structure models from electron-density maps produced via X-ray crystallography. ACMI uses a Markov Random Field to model the three-dimensional (3D) location of each non-hydrogen atom in a protein. Calculating the best structure in this model is intractable, so ACMI uses approximate inference methods to estimate the optimal structure. While previous results have shown ACMI to be the state-of-the-art method on this task, its approximate inference algorithm remains computationally expensive and susceptible to errors. In this work, we develop Probabilistic Ensembles in ACMI (PEA), a framework for leveraging multiple, independent runs of approximate inference to produce estimates of protein structures. Our results show statistically significant improvements in the accuracy of inference resulting in more complete and accurate protein structures. In addition, PEA provides a general framework for advanced approximate inference methods in complex problem domains.

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