[HTML][HTML] Deep learning methods in protein structure prediction

M Torrisi, G Pollastri, Q Le - Computational and structural biotechnology …, 2020‏ - Elsevier
Abstract Protein Structure Prediction is a central topic in Structural Bioinformatics. Since
the'60s statistical methods, followed by increasingly complex Machine Learning and recently …

Toward the solution of the protein structure prediction problem

R Pearce, Y Zhang - Journal of Biological Chemistry, 2021‏ - jbc.org
Since Anfinsen demonstrated that the information encoded in a protein's amino acid
sequence determines its structure in 1973, solving the protein structure prediction problem …

Predicting protein residue–residue contacts using deep networks and boosting

J Eickholt, J Cheng - Bioinformatics, 2012‏ - academic.oup.com
Motivation: Protein residue–residue contacts continue to play a larger and larger role in
protein tertiary structure modeling and evaluation. Yet, while the importance of contact …

Generating tertiary protein structures via interpretable graph variational autoencoders

X Guo, Y Du, S Tadepalli, L Zhao… - Bioinformatics …, 2021‏ - academic.oup.com
Motivation Modeling the structural plasticity of protein molecules remains challenging. Most
research has focused on obtaining one biologically active structure. This includes the recent …

Artificial intelligence for template-free protein structure prediction: a comprehensive review

MMM Mufassirin, MAH Newton, A Sattar - Artificial Intelligence Review, 2023‏ - Springer
Protein structure prediction (PSP) is a grand challenge in bioinformatics, drug discovery, and
related fields. PSP is computationally challenging because of an astronomically large …

A roadmap for big model

S Yuan, H Zhao, S Zhao, J Leng, Y Liang… - arxiv preprint arxiv …, 2022‏ - arxiv.org
With the rapid development of deep learning, training Big Models (BMs) for multiple
downstream tasks becomes a popular paradigm. Researchers have achieved various …

Toward an accurate prediction of inter-residue distances in proteins using 2D recursive neural networks

P Kukic, C Mirabello, G Tradigo, I Walsh, P Veltri… - BMC …, 2014‏ - Springer
Background Protein inter-residue contact maps provide a translation and rotation invariant
topological representation of a protein. They can be used as an intermediary step in protein …

Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8

I Ezkurdia, O Grana, JMG Izarzugaza… - Proteins: Structure …, 2009‏ - Wiley Online Library
This article details the assessment process and evaluation results for two categories in the
8th Critical Assessment of Protein Structure Prediction experiment (CASP8). The domain …

DeepCDpred: Inter-residue distance and contact prediction for improved prediction of protein structure

S Ji, T Oruç, L Mead, MF Rehman, CM Thomas… - PloS one, 2019‏ - journals.plos.org
Rapid, accurate prediction of protein structure from amino acid sequence would accelerate
fields as diverse as drug discovery, synthetic biology and disease diagnosis. Massively …

[HTML][HTML] Recent applications of deep learning methods on evolution-and contact-based protein structure prediction

D Suh, JW Lee, S Choi, Y Lee - International Journal of Molecular …, 2021‏ - mdpi.com
The new advances in deep learning methods have influenced many aspects of scientific
research, including the study of the protein system. The prediction of proteins' 3D structural …