TY - JOUR
T1 - A novel geometry-based approach to infer protein interface similarity
AU - Budowski-Tal, Inbal
AU - Kolodny, Rachel
AU - Mandel-Gutfreund, Yael
N1 - Publisher Copyright:
© 2018 The Author(s).
PY - 2018/12/1
Y1 - 2018/12/1
N2 - The protein interface is key to understand protein function, providing a vital insight on how proteins interact with each other and with other molecules. Over the years, many computational methods to compare protein structures were developed, yet evaluating interface similarity remains a very difficult task. Here, we present PatchBag - a geometry based method for efficient comparison of protein surfaces and interfaces. PatchBag is a Bag-Of-Words approach, which represents complex objects as vectors, enabling to search interface similarity in a highly efficient manner. Using a novel framework for evaluating interface similarity, we show that PatchBag performance is comparable to state-of-the-art alignment-based structural comparison methods. The great advantage of PatchBag is that it does not rely on sequence or fold information, thus enabling to detect similarities between interfaces in unrelated proteins. We propose that PatchBag can contribute to reveal novel evolutionary and functional relationships between protein interfaces.
AB - The protein interface is key to understand protein function, providing a vital insight on how proteins interact with each other and with other molecules. Over the years, many computational methods to compare protein structures were developed, yet evaluating interface similarity remains a very difficult task. Here, we present PatchBag - a geometry based method for efficient comparison of protein surfaces and interfaces. PatchBag is a Bag-Of-Words approach, which represents complex objects as vectors, enabling to search interface similarity in a highly efficient manner. Using a novel framework for evaluating interface similarity, we show that PatchBag performance is comparable to state-of-the-art alignment-based structural comparison methods. The great advantage of PatchBag is that it does not rely on sequence or fold information, thus enabling to detect similarities between interfaces in unrelated proteins. We propose that PatchBag can contribute to reveal novel evolutionary and functional relationships between protein interfaces.
UR - http://www.scopus.com/inward/record.url?scp=85047970388&partnerID=8YFLogxK
U2 - 10.1038/s41598-018-26497-z
DO - 10.1038/s41598-018-26497-z
M3 - Article
C2 - 29844500
AN - SCOPUS:85047970388
SN - 2045-2322
VL - 8
JO - Scientific Reports
JF - Scientific Reports
IS - 1
M1 - 8192
ER -