AI-based protein structure databases have the potential to accelerate rare diseases research: AlphaFoldDB and the case of IAHSP/Alsin

We propose new methods for finding similarities in protein structure databases. These methods extract feature vectors on triplets of SSEs (Secondary Structure Elements) of proteins. The feature vectors are then indexed using a multidimensional index structure. Our first technique considers the problem of finding proteins similar to a given query protein in a protein dataset. It quickly finds promising proteins using the index structure. These proteins are then aligned to the query protein using a popular pairwise alignment tool such as VAST. We also develop a novel statistical model to estimate the goodness of a match using the SSEs. Our second technique considers the problem of joining two protein datasets to find an all-to-all similarity. Experimental results show that our techniques improve the pruning time of VAST 3 to 3.5 times, while keeping the sensitivity similar. Our technique can also be incorporated with DALI and CE to improve their running times by a factor of 2 and 2.7 respectively. The software is available online at .

Download Full-text

Improving classification in protein structure databases using text mining

BMC Bioinformatics ◽

10.1186/1471-2105-10-129 ◽

2009 ◽

Vol 10 (1) ◽

pp. 129 ◽

Cited By ~ 11

Author(s):

Antonis Koussounadis ◽

Oliver C Redfern ◽

David T Jones

Keyword(s):

Protein Structure ◽

Text Mining ◽

Structure Databases

Download Full-text

Analytical tools in protein structure determination

International Journal of Pharmaceutical Chemistry and Analysis ◽

10.18231/j.ijpca.2021.021 ◽

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.

Download Full-text