Amino acid substitution matrices based on 4-body Delaunay contact profiles

Date

2007-10-17

Author

Sacan, Ahmet
Toroslu, İsmail Hakkı

Metadata

Show full item record

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Item Usage Stats

125
views

0
downloads

Sequence similarity search of proteins is one of the basic and most common steps followed in bioninformatics research and is used in making evolutionary, structural, and functional inferences. The quality of the search and the alignment of the protein sequences depend crucially on the underlying amino-acid substitution matrix. We present a method for deriving amino acid substitution matrices from 4-body contact propensities of amino-acids in 3D protein structures. Unlike current popular methods, our method does not rely on mutational analysis, evolutionary arguments, or alignment of protein sequences or structures. The alignment accuracy of our derived matrices is evaluated using the BAliBASE reference alignment set and is found to be comparable to that of popular matrices from the literature. Notably, the metric subset of our matrices outperform other available metric matrices. Our matrices will be useful especially in the development of empirical potential energy functions and in distance-based sequence indexing.

Subject Keywords

Protein structure, Delaunay tessellation, Similarity search, Sequence alignment, Amino acid substitution matrix, Metric matrix

URI

https://hdl.handle.net/11511/46827

DOI

https://doi.org/10.1109/bibe.2007.4375651

Collections

Department of Computer Engineering, Conference / Seminar

Suggestions

OpenMETU
Core

Distance-based Indexing of Residue Contacts for Protein Structure Retrieval and Alignment Sacan, Ahmet; Toroslu, İsmail Hakkı; Ferhatosmanoglu, Hakan (2008-10-10) New protein structures are continuously being determined with the hope of deriving insights into the function and mechanisms of proteins, and consequently, protein structure repositories are growing by leaps and bounds. However, we are still far from having the right methods for sensitive and effective use of the available structural data. The fact that current structural analysis tools are impractical for large-scale applications have given rise to several approaches that try to quickly identify candidate ...
AMINO-ACID SUBSTITUTIONS WITHIN THE ANALOGOUS NUCLEOTIDE-BINDING LOOP (P-LOOP) OF AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE-II KOCABIVIK, S; PERLIN, MH (Elsevier BV, 1994-01-01) 1. Oligonucleotide-directed mutagenesis of APH(3')-II was used to investigate the functions of key amino acids in the P-loop analogous motif of the enzyme. 2. The mutations of Gly205 --> GIu, Gly210 --> Ala and Arg211 --> Pro considerably reduced the resistance of the resulting strains to KM and to related drugs, e.g. G418. 3. Similarly, enzyme activity in the crude extracts of these mutants was substantially reduced as well as the enzyme's affinity for Mg2+ ATP. 4. Alternatively substitutions at a highly c...
Arginine-aromatic interactions and their effects on arginine-induced solubilization of aromatic solutes and suppression of protein aggregation Shah, Dhawal; Li, Jianguo; Shaikh, Abdul Rajjak; Rajagopalan, Raj (2012-01-01) We examine the interaction of aromatic residues of proteins with arginine, an additive commonly used to suppress protein aggregation, using experiments and molecular dynamics simulations. An aromatic-rich peptide, FFYTP (a segment of insulin), and lysozyme and insulin are used as model systems. Mass spectrometry shows that arginine increases the solubility of FFYTP by binding to the peptide, with the simulations revealing the predominant association of arginine to be with the aromatic residues. The calculat...
Prediction of protein subcellular localization based on primary sequence data Özarar, Mert; Atalay, Mehmet Volkan; Department of Computer Engineering (2003) Subcellular localization is crucial for determining the functions of proteins. A system called prediction of protein subcellular localization (P2SL) that predicts the subcellular localization of proteins in eukaryotic organisms based on the amino acid content of primary sequences using amino acid order is designed. The approach for prediction is to nd the most frequent motifs for each protein in a given class based on clustering via self organizing maps and then to use these most frequent motifs as features...
Multi-view subcellular localization prediction of human proteins Özsarı, Gökhan; Atalay, M. Volkan.; Department of Computer Engineering (2019) Determining the subcellular localization of proteins is crucial for Understanding the functions of proteins, drug targeting, systems biology, and proteomics research. Experimental validation of subcellular localization is an expensive and challenging process. There exist several computational methods for automated prediction of protein subcellular localization; however, there is still room for better performance. Here, we propose a multi-view SVM-based approach that provides predictions for human proteins. ...

Citation Formats

A. Sacan and İ. H. Toroslu, “Amino acid substitution matrices based on 4-body Delaunay contact profiles,” 2007, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/46827.