A review of methods available to estimate solvent-accessible surface areas of soluble proteins in the folded and unfolded states

S Ausaf Ali, M Imtaiyaz Hassan, A Islam… - Current Protein and …, 2014 - benthamdirect.com
Solvent accessible surface area (SASA) of proteins has always been considered as a
decisive factor in protein folding and stability studies. It is defined as the surface …

DeepSVM-fold: protein fold recognition by combining support vector machines and pairwise sequence similarity scores generated by deep learning networks

B Liu, CC Li, K Yan - Briefings in bioinformatics, 2020 - academic.oup.com
Protein fold recognition is critical for studying the structures and functions of proteins. The
existing protein fold recognition approaches failed to efficiently calculate the pairwise …

Protein sequence comparison and fold recognition: progress and good-practice benchmarking

J Söding, M Remmert - Current opinion in structural biology, 2011 - Elsevier
Protein sequence comparison methods have grown increasingly sensitive during the last
decade and can often identify distantly related proteins sharing a common ancestor some 3 …

Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties …

Y Yang, E Faraggi, H Zhao, Y Zhou - Bioinformatics, 2011 - academic.oup.com
Motivation: In recent years, development of a single-method fold-recognition server lags
behind consensus and multiple template techniques. However, a good consensus …

[HTML][HTML] iStable 2.0: Predicting protein thermal stability changes by integrating various characteristic modules

CW Chen, MH Lin, CC Liao, HP Chang… - Computational and …, 2020 - Elsevier
Protein mutations can lead to structural changes that affect protein function and result in
disease occurrence. In protein engineering, drug design or and optimization industries …

MotifCNN-fold: protein fold recognition based on fold-specific features extracted by motif-based convolutional neural networks

CC Li, B Liu - Briefings in bioinformatics, 2020 - academic.oup.com
Protein fold recognition is one of the most critical tasks to explore the structures and
functions of the proteins based on their primary sequence information. The existing protein …

[HTML][HTML] Improving protein fold recognition by deep learning networks

T Jo, J Hou, J Eickholt, J Cheng - Scientific reports, 2015 - nature.com
For accurate recognition of protein folds, a deep learning network method (DN-Fold) was
developed to predict if a given query-template protein pair belongs to the same structural …

FoldRec-C2C: protein fold recognition by combining cluster-to-cluster model and protein similarity network

J Shao, K Yan, B Liu - Briefings in bioinformatics, 2021 - academic.oup.com
As a key for studying the protein structures, protein fold recognition is playing an important
role in predicting the protein structures associated with COVID-19 and other important …

ProtFold-DFG: protein fold recognition by combining Directed Fusion Graph and PageRank algorithm

J Shao, B Liu - Briefings in Bioinformatics, 2021 - academic.oup.com
As one of the most important tasks in protein structure prediction, protein fold recognition has
attracted more and more attention. In this regard, some computational predictors have been …

Fold-LTR-TCP: protein fold recognition based on triadic closure principle

B Liu, Y Zhu, K Yan - Briefings in Bioinformatics, 2020 - academic.oup.com
As an important task in protein structure and function studies, protein fold recognition has
attracted more and more attention. The existing computational predictors in this field treat …