Proteins and their interacting partners: An introduction to protein–ligand binding site prediction methods

DB Roche, DA Brackenridge, LJ McGuffin - International journal of …, 2015 - mdpi.com
Elucidating the biological and biochemical roles of proteins, and subsequently determining
their interacting partners, can be difficult and time consuming using in vitro and/or in vivo …

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Y Jiang, TR Oron, WT Clark, AR Bankapur, D D'Andrea… - Genome biology, 2016 - Springer
Background A major bottleneck in our understanding of the molecular underpinnings of life
is the assignment of function to proteins. While molecular experiments provide the most …

Computational approaches to predict protein functional families and functional sites

C Rauer, N Sen, VP Waman, M Abbasian… - Current Opinion in …, 2021 - Elsevier
Understanding the mechanisms of protein function is indispensable for many biological
applications, such as protein engineering and drug design. However, experimental …

Protein functional annotation of simultaneously improved stability, accuracy and false discovery rate achieved by a sequence-based deep learning

J Hong, Y Luo, Y Zhang, J Ying, W Xue… - Briefings in …, 2020 - academic.oup.com
Functional annotation of protein sequence with high accuracy has become one of the most
important issues in modern biomedical studies, and computational approaches of …

NetGO: improving large-scale protein function prediction with massive network information

R You, S Yao, Y Xiong, X Huang, F Sun… - Nucleic acids …, 2019 - academic.oup.com
Automated function prediction (AFP) of proteins is of great significance in biology. AFP can
be regarded as a problem of the large-scale multi-label classification where a protein can be …

SVM-Prot 2016: a web-server for machine learning prediction of protein functional families from sequence irrespective of similarity

YH Li, JY Xu, L Tao, XF Li, S Li, X Zeng, SY Chen… - PloS one, 2016 - journals.plos.org
Knowledge of protein function is important for biological, medical and therapeutic studies,
but many proteins are still unknown in function. There is a need for more improved functional …

Domain-PFP allows protein function prediction using function-aware domain embedding representations

N Ibtehaz, Y Kagaya, D Kihara - Communications Biology, 2023 - nature.com
Abstract Domains are functional and structural units of proteins that govern various
biological functions performed by the proteins. Therefore, the characterization of domains in …

GoFDR: a sequence alignment based method for predicting protein functions

Q Gong, W Ning, W Tian - Methods, 2016 - Elsevier
In this study, we developed a method named GoFDR for predicting Gene Ontology (GO)-
based protein functions. The input for GoFDR is simply a query sequence-based multiple …

Investigation of antidepressant properties of yohimbine by employing structure-based computational assessments

M Tasleem, A Alrehaily, TM Almeleebia… - Current Issues in …, 2021 - mdpi.com
The use of pharmaceuticals to treat Major Depressive Disorder (MDD) has several
drawbacks, including severe side effects. Natural compounds with great efficacy and few …

DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web

M Kulmanov, F Zhapa-Camacho… - Nucleic Acids …, 2021 - academic.oup.com
Understanding the functions of proteins is crucial to understand biological processes on a
molecular level. Many more protein sequences are available than can be investigated …