Contrastive representation learning for 3d protein structures
P Hermosilla, T Ropinski - arXiv preprint arXiv:2205.15675, 2022 - arxiv.org
Learning from 3D protein structures has gained wide interest in protein modeling and
structural bioinformatics. Unfortunately, the number of available structures is orders of …
structural bioinformatics. Unfortunately, the number of available structures is orders of …
[HTML][HTML] Fast protein structure comparison through effective representation learning with contrastive graph neural networks
C Xia, SH Feng, Y Xia, X Pan… - PLoS computational …, 2022 - journals.plos.org
Protein structure alignment algorithms are often time-consuming, resulting in challenges for
large-scale protein structure similarity-based retrieval. There is an urgent need for more …
large-scale protein structure similarity-based retrieval. There is an urgent need for more …
FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately
I Budowski-Tal, Y Nov… - Proceedings of the …, 2010 - National Acad Sciences
Fast identification of protein structures that are similar to a specified query structure in the
entire Protein Data Bank (PDB) is fundamental in structure and function prediction. We …
entire Protein Data Bank (PDB) is fundamental in structure and function prediction. We …
Learning structural motif representations for efficient protein structure search
Motivation Given a protein of unknown function, fast identification of similar protein structures
from the Protein Data Bank (PDB) is a critical step for inferring its biological function. Such …
from the Protein Data Bank (PDB) is a critical step for inferring its biological function. Such …
[HTML][HTML] Zero-shot prediction of mutation effects with multimodal deep representation learning guides protein engineering
P Cheng, C Mao, J Tang, S Yang, Y Cheng, W Wang… - Cell Research, 2024 - nature.com
Mutations in amino acid sequences can provoke changes in protein function. Accurate and
unsupervised prediction of mutation effects is critical in biotechnology and biomedicine, but …
unsupervised prediction of mutation effects is critical in biotechnology and biomedicine, but …
Multi-view methods for protein structure comparison using latent dirichlet allocation
S Shivashankar, S Srivathsan, B Ravindran… - …, 2011 - academic.oup.com
Motivation: With rapidly expanding protein structure databases, efficiently retrieving
structures similar to a given protein is an important problem. It involves two major issues:(i) …
structures similar to a given protein is an important problem. It involves two major issues:(i) …
Rapid retrieval of protein structures from databases
Z Aung, KL Tan - Drug Discovery Today, 2007 - Elsevier
As protein databases continue to grow in size, exhaustive search methods that compare a
query structure against every database structure can no longer provide satisfactory …
query structure against every database structure can no longer provide satisfactory …
Searching for three-dimensional secondary structural patterns in proteins with ProSMoS
S Shi, Y Zhong, I Majumdar, S Sri Krishna… - …, 2007 - academic.oup.com
Motivation: Many evolutionarily distant, but functionally meaningful links between proteins
come to light through comparison of spatial structures. Most programs that assess structural …
come to light through comparison of spatial structures. Most programs that assess structural …
Persistent homology reveals strong phylogenetic signal in 3D protein structures
L Bou Dagher, D Madern, P Malbos… - PNAS …, 2024 - academic.oup.com
Abstract Changes that occur in proteins over time provide a phylogenetic signal that can be
used to decipher their evolutionary history and the relationships between organisms …
used to decipher their evolutionary history and the relationships between organisms …
ProSMoS server: a pattern-based search using interaction matrix representation of protein structures
S Shi, B Chitturi, NV Grishin - Nucleic acids research, 2009 - academic.oup.com
Assessing structural similarity and defining common regions through comparison of protein
spatial structures is an important task in functional and evolutionary studies of proteins …
spatial structures is an important task in functional and evolutionary studies of proteins …