SBSM-Pro: support bio-sequence machine for proteins

doi:10.1007/s11432-024-4171-9

2024-10-22

PRE

DOI：10.1007/s11432-024-4171-9

原文链接

原文求助

摘要

En 中文

Proteins play a pivotal role in biological systems. The use of machine learning algorithms for protein classification can assist and even guide biological experiments, offering crucial insights for biotechnological applications. We introduce the support bio-sequence machine for proteins (SBSM-Pro), a model purpose-built for the classification of biological sequences. This model starts with raw sequences and groups amino acids based on their physicochemical properties. It incorporates sequence alignment to measure the similarities between proteins and uses a novel multiple kernel learning (MKL) approach to integrate various types of information, utilizing support vector machines for classification prediction. The results indicate that our model demonstrates commendable performance across ten datasets in terms of the identification of protein function and post translational modification. This research not only exemplifies state-of-the-art work in protein classification but also paves avenues for new directions in this domain, representing a beneficial endeavor in the development of platforms tailored for the classification of biological sequences. SBSM-Pro is available for access at http://lab.malab.cn/soft/SBSM-Pro/.

Keyword:

protein classification

machine learning

multiple kernel learning

sequence alignment

期刊

Science China Information Sciences

IF:

7.6

论文数:

4.9K

被引数:

8.9K

机构

暂无机构信息

引用论文

Deepro-Glu: combination of convolutional neural network and Bi-LSTM models using ProtBert and handcrafted features to identify lysine glutarylation sites Deepro-glu: 使用ProtBert和手工制作的特征结合卷积神经网络和bi-lstm模型来识别赖氨酸谷氨酰胺化位点

BRIEFINGS IN BIOINFORMATICS

IF7.7

2023-01-18

PREAI

Wang, Xiao; Ding, Zhaoyuan; Wang, Rong; Lin, Xi

Intermittently chaotic oscillations for a differential-delay equation with Gaussian nonlinearity

Physical Review A

IF0

1992-01-01

PREAI

Ian Hamilton

Isolation and identification of antibiotic albaflavenone from Dictyophora indusiata (Vent: Pers.) Fischer

Journal of Chemical Research

IF0

2011-11-01

OAAI

Mingquan Huang; Xi Chen; Hongyu Tian; Baoguo Sun; Haitao Chen

International Medical Travelers, Length of Stay, and the Continuum of Care

Quality Management in Health Care

IF0

2011-01-01

PREAI

Siriporn Patricia Satjapot; Tricia J. Johnson; Andrew N. Garman

Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain

GENOME BIOLOGY

IF9.4

2017-01-05

241

OAAI

Amort, Thomas; Rieder, Dietmar; Wille, Alexandra; Khokhlova-Cubberley, Daria; Riml, Christian; Trixl, Lukas; Jia, Xi-Yu; Micura, Ronald; Lusser, Alexandra

DaDL-SChlo: protein subchloroplast localization prediction based on generative adversarial networks and pre-trained protein language model

BRIEFINGS IN BIOINFORMATICS

IF7.7

2023-03-17

PREAI

Wang, Xiao; Han, Lijun; Wang, Rong; Chen, Haoran

Quantitative Assays of Mdm2 Ubiquitin Ligase Activity and Other Ubiquitin‐Utilizing Enzymes for Inhibitor Discovery

Methods in Enzymology

IF0

2005-01-01

PREAI

Kurt R. Auger; Robert A. Copeland; Zhihong Lai