PPInterface: A Comprehensive Dataset of 3D Protein-Protein Interface Structures

被引：0

作者：

Abali, Zeynep ^{[1
]}

Aydin, Zeynep ^{[1
]}

Khokhar, Moaaz ^{[3
]}

Ates, Yigit Can ^{[3
]}

Gursoy, Attila ^{[3
]}

Keskin, Ozlem ^{[2
]}

机构：

[1] Koc Univ, Computat Sci & Engn Grad Program, TR-34450 Istanbul, Turkiye

[2] Koc Univ, Chem & Biol Engn, TR-34450 Istanbul, Turkiye

[3] Koc Univ, Comp Engn, TR-34450 Istanbul, Turkiye

来源：

JOURNAL OF MOLECULAR BIOLOGY | 2024年 / 436卷 / 17期

关键词：

Protein interfaces; Dataset; Protein-protein complexes; Protein-protein interactions; Interface visualization; 3D Protein-protein interface dataset; MOLECULAR-BIOLOGY; DATABASE; CLASSIFICATION;

D O I：

10.1016/j.jmb.2024.168686

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The PPInterface dataset contains 815,082 interface structures, providing the most comprehensive structural information on protein-protein interfaces. This resource is extracted from over 215,000 threedimensional protein structures stored in the Protein Data Bank (PDB). The dataset contains a wide range of protein complexes, providing a wealth of information for researchers investigating the structural properties of protein-protein interactions. The accompanying web server has a user-friendly interface that allows for efficient search and download functions. Researchers can access detailed information on protein interface structures, visualize them, and explore a variety of features, increasing the dataset's utility and accessibility. The dataset and web server can be found at https://3dpath.ku.edu.tr/PPInt/. (c) 2024 Published by Elsevier Ltd.

引用

页数：7

共 50 条

[31] Binding of small molecules at interface of protein-protein complex - A newer approach to rational drug design
Gurung, A. B.
Bhattacharjee, A.
Ali, M. Ajmal
Al-Hemaid, F.
Lee, Joongku
SAUDI JOURNAL OF BIOLOGICAL SCIENCES, 2017, 24 (02) : 379 - 388
[32] A soft docking algorithm for predicting the structures of protein-protein complexes
Li, CH
Ma, XH
Chen, WZ
Wang, CX
ACTA BIOCHIMICA ET BIOPHYSICA SINICA, 2003, 35 (01): : 35 - 40
[33] Comprehensive host-pathogen protein-protein interaction network analysis
Khorsand, Babak
Savadi, Abdorreza
Naghibzadeh, Mahmoud
BMC BIOINFORMATICS, 2020, 21 (01)
[34] HVIDB: a comprehensive database for human-virus protein-protein interactions
Yang, Xiaodi
Lian, Xianyi
Fu, Chen
Wuchty, Stefan
Yang, Shiping
Zhang, Ziding
BRIEFINGS IN BIOINFORMATICS, 2021, 22 (02) : 832 - 844
[35] iWRAP: An Interface Threading Approach with Application to Prediction of Cancer-Related Protein-Protein Interactions
Hosur, Raghavendra
Xu, Jinbo
Bienkowska, Jadwiga
Berger, Bonnie
JOURNAL OF MOLECULAR BIOLOGY, 2011, 405 (05) : 1295 - 1310
[36] Interdiction at a protein-protein interface: MCL-1 inhibitors for oncology
Li, Kexue
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 2021, 32
[37] Scoring of protein-protein docking models utilizing predicted interface residues
Pozzati, Gabriele
Kundrotas, Petras
Elofsson, Arne
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2022, 90 (07) : 1493 - 1505
[38] An exploration of the 3D chemical space has highlighted a specific shape profile for the compounds intended to inhibit protein-protein interactions
Kuenemann, Melaine A.
Bourbon, Laura M. L.
Labbe, Celine M.
Villoutreix, Bruno O.
Sperandio, Olivier
BMC BIOINFORMATICS, 2015, 16
[39] Binding interface change and cryptic variation in the evolution of protein-protein interactions
Ames, Ryan M.
Talavera, David
Williams, Simon G.
Robertson, David L.
Lovell, Simon C.
BMC EVOLUTIONARY BIOLOGY, 2016, 16
[40] Protein-protein Interaction Prediction using Desolvation Energies and Interface Properties
Rueda, Luis
Banerjee, Sridip
Aziz, Md. Mominul
Raza, Mohammad
2010 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE, 2010, : 17 - 22

← 1 2 3 4 5 →