A dataset of protein-protein interfaces for drug repurposing

Download

HIBIT22_paper_94.pdf

Date

2022-10

Author

Abalı, Zeynep
Gursoy, Attila
Keskin, Özlem

Metadata

Show full item record

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

Item Usage Stats

56
views

34
downloads

Proteins have crucial functions in many processes, ranging from structural building blocks to signaling or acting as catalysts to store and transport different molecules. Most functions of proteins are not conducted in isolation by a monomer (a single chain of protein structure) but with the interaction of multiple partners. Understanding the structural architecture of protein interfaces is one of the key challenges in explaining how proteins interact and function. Considering the crucial functions of proteins, proteinprotein interfaces can be important targets for drug discovery and repurposing studies; this is only possible if the structural data available can be utilized in a complete, biologically correct, and technically accessible manner. Protein Data Bank (PDB) is an invaluable resource for protein structures, but it is highly redundant in nature. In this study, we analyzed interface structures from PDB; we compared protein-protein interfaces with respect to amino acid sequences of their chains, and we compared sequentially unique interfaces structurally to form a unique set of interface representatives as a dataset for further studies.

URI

https://hibit2022.ims.metu.edu.tr
https://hdl.handle.net/11511/101860

Conference Name

The International Symposium on Health Informatics and Bioinformatics

Collections

Graduate School of Informatics, Conference / Seminar

Suggestions

OpenMETU
Core

A Structural Perspective on the Modulation of Protein-Protein Interactions with Small Molecules. Demirel, Habibe Cansu; Dogan, Tunca; Tunçbağ, Nurcan (2018-01-01) Protein-Protein Interactions (PPIs) are the key components in many cellular processes including signaling pathways, enzymatic reactions and epigenetic regulation. Abnormal interactions of some proteins may be pathogenic and cause various disorders including cancer and neurodegenerative diseases. Although inhibiting PPIs with small molecules is a challenging task, it gained an increasing interest because of its strong potential for drug discovery and design. The knowledge of the interface as well as the stru...
A novel model-based method for feature extraction from protein sequences for classification Sarac, Omer Sinan; Atalay, Mehmet Volkan; Atalay, Rengül (2006-01-01) Representation of amino-acid sequences constitutes the key point in classification of proteins into functional or structural classes. The representation should contain the biologically meaningful information hidden in the primary sequence of the protein. Conserved or similar subsequences are strong indicators of functional and structural similarity. In this study we present a feature mapping that takes into account the models of the subsequences of protein sequences. An expectation-maximization algorithm al...
A computational framework of configurational-force-driven brittle fracture based on incremental energy minimization MIEHE, CHRISTIAN; Gürses, Ercan; BIRKLE, MANUEL (Springer Science and Business Media LLC, 2007-06-01) A variational formulation of quasi-static brittle fracture in elastic solids at small strains is proposed and an associated finite element implementation is presented. On the theoretical side, a consistent thermodynamic framework for brittle crack propagation is outlined. It is shown that both the elastic equilibrium response as well as the local crack evolution follow in a natural format by exploitation of a global Clausius-Planck inequality. Here, the canonical direction of the crack propagation associate...
A computer program for the analysis of 1-D contaminant migration through a soil layer Çokça, Erdal (Elsevier BV, 2003-01-01) The physical and chemical processes that influence contaminant transport through a saturated soil layer are presented. The computer program (1DContr) was developed based on existing analytical solutions for one-dimensional transport of contaminants in a saturated soil layer. The computer program is given for pulse and continuous source. The formulation includes advective and dispersive transport as well as sorption and first order transformation. The computer program that is based on analytical solutions is...
A density functional theory study on the structures and energetics of CdmTen clusters (m + n <= 6) Pekoz, Rengin; Erkoç, Şakir (Elsevier BV, 2009-06-01) Density functional method has been used to study the structural features and energetics of CdmTen clusters (m + n <= 6). The results presented include the geometric structures, binding energies, Mulliken charges on atoms, vibrational frequencies and the corresponding non-zero infrared intensities, HOMO-LUMO energies and the frontier molecular orbital energy gaps, the most possible dissociation channels and their corresponding energies of the clusters.

Citation Formats

Z. Abalı, A. Gursoy, and Ö. Keskin, “A dataset of protein-protein interfaces for drug repurposing,” Erdemli, Mersin, TÜRKİYE, 2022, p. 3094, Accessed: 00, 2023. [Online]. Available: https://hibit2022.ims.metu.edu.tr.