Match-Communications in Mathematical and in Computer Chemistry最新文献_第4页

Fer-COCL: A Novel Method Based on Multiple Deep Learning Algorithms for Identifying Fertility-Related Proteins ferc - cocl:一种基于多个深度学习算法的鉴定生育相关蛋白的新方法

IF 2.6 2区化学

Match-Communications in Mathematical and in Computer Chemistry Pub Date : 2023-07-01 DOI: 10.46793/match.90-3.537z

Shenmin Zhang, Xinjie Li, Hongyan Shi, Yuanyuan Jing, Yunyun Liang, Yusen Zhang

{"title":"Fer-COCL: A Novel Method Based on Multiple Deep Learning Algorithms for Identifying Fertility-Related Proteins","authors":"Shenmin Zhang, Xinjie Li, Hongyan Shi, Yuanyuan Jing, Yunyun Liang, Yusen Zhang","doi":"10.46793/match.90-3.537z","DOIUrl":"https://doi.org/10.46793/match.90-3.537z","url":null,"abstract":"The survival of species depends on the fertility of organisms. It is also worthwhile to study the proteins that can regulate the reproductive activity of organisms. Since biological experiments are laborious to confirm proteins, it has become a priority that develop relevant computational models to predict the function of fertility-related proteins. With the development of machine learning, pertinent various algorithms can be the key to identifying fertility-related proteins. In this work, we develop a model Fer-COCL based on deep learning. The model consists of multiple features as well as multiple deep learning algorithms. First, we extract features using Amino acid composition (AAC), Dipeptide composition (DPC), CTD transition (CTDT) and deviation between the dipeptide and the expected mean (DDE). After that, the spliced features are fed into the classifier. The data processed jointly by convolutional neural network and long short-term memory is input to the fully connected layer for classification. After evaluating the model using 10-fold cross-validation, the accuracy of the two data sets reaches 97.1% and 98.3%, respectively. The results indicate that the model is efficient and accurate, facilitating biologists' research on biological fertility. In addition, a free online tool for predicting the function of fertility-related proteins is available at http://fercocl.zhanglab.site/.","PeriodicalId":51115,"journal":{"name":"Match-Communications in Mathematical and in Computer Chemistry","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80134941","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Estrada and L-Estrada Indices of a Graph and Their Relationship with the Number of Spanning Trees 图的Estrada和L-Estrada指标及其与生成树数目的关系

IF 2.6 2区化学

Match-Communications in Mathematical and in Computer Chemistry Pub Date : 2023-07-01 DOI: 10.46793/match.90-3.787a

Mahsa Arabzadeh, G. Fath-Tabar, Hamid Rasoli, A. Tehranian

引用次数: 0

A Note on an Inequality Between Energy and Sombor Index of a Graph 图的能量与Sombor指数不等的一个注记

IF 2.6 2区化学

Match-Communications in Mathematical and in Computer Chemistry Pub Date : 2023-07-01 DOI: 10.46793/match.90-3.765a

S. Akbari, M. Habibi, Soheyr Rouhani

引用次数: 0

On the Harary Index of Graphs with Given Dissociation Number 给定解离数图的哈里索引

IF 2.6 2区化学

Match-Communications in Mathematical and in Computer Chemistry Pub Date : 2023-07-01 DOI: 10.46793/match.90-3.649h

Jing Huang, Minjie Zhang

引用次数: 0

A Novel Fast Approach for Protein Classification and Evolutionary Analysis 一种新的快速蛋白质分类和进化分析方法

IF 2.6 2区化学

Match-Communications in Mathematical and in Computer Chemistry Pub Date : 2023-04-01 DOI: 10.46793/match.90-2.381a

Liang Ai, Jie Feng, Yu-Hua Yao

引用次数: 0

Kashuri Fundo Decomposition Method for Solving Michaelis-Menten Nonlinear Biochemical Reaction Model 求解Michaelis-Menten非线性生化反应模型的Kashuri Fundo分解法

IF 2.6 2区化学

Match-Communications in Mathematical and in Computer Chemistry Pub Date : 2023-04-01 DOI: 10.46793/match.90-2.315p

H. Peker, Fatma Aybike Çuha, Bilge Peker

{"title":"Kashuri Fundo Decomposition Method for Solving Michaelis-Menten Nonlinear Biochemical Reaction Model","authors":"H. Peker, Fatma Aybike Çuha, Bilge Peker","doi":"10.46793/match.90-2.315p","DOIUrl":"https://doi.org/10.46793/match.90-2.315p","url":null,"abstract":"In most of the real life problems, we encounter with nonlinear differential equations. Problems are made more understandable by modeling them with these equations. In this way, it becomes easier to interpret the problems and reach the results. In 1913, the basic enzymatic reaction model introduced by Michaelis and Menten to describe enzyme processes is an example of nonlinear differential equation. This model is the one of the simplest and best-known approaches of the mechanisms used to model enzyme-catalyzed reactions and is the most studied. For most nonlinear differential equations, it is very difficult to get an analytical solution. For this reason, various studies have been carried out to find approximate solutions to such equations. Among these studies, those in which two different methods are used by blending attract attention. In this study, a blended form of the Kashuri Fundo transform method and the Adomian decomposition method, so-called the Kashuri Fundo decomposition method, is used to find a solution to the Michaelis-Menten nonlinear biochemical reaction model in this way. This method has been applied to the biochemical reaction model and an approximate solution has been obtained for this model without complex calculations. This shows that the hybrid method is an effective, reliable, simpler and time-saving method in reaching the solutions of nonlinear differential equations.","PeriodicalId":51115,"journal":{"name":"Match-Communications in Mathematical and in Computer Chemistry","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74466097","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Persistent Subspaces of Reaction-Based Dynamical Systems 基于反应的动力系统的持久子空间

IF 2.6 2区化学

Match-Communications in Mathematical and in Computer Chemistry Pub Date : 2023-04-01 DOI: 10.46793/match.90-2.471i

B. Ibrahim, Stephan Peter

{"title":"Persistent Subspaces of Reaction-Based Dynamical Systems","authors":"B. Ibrahim, Stephan Peter","doi":"10.46793/match.90-2.471i","DOIUrl":"https://doi.org/10.46793/match.90-2.471i","url":null,"abstract":"Various types of dynamical systems, such as ordinary differential equations (ODEs) or partial differential equations (PDEs), are widely applied not only in chemistry but also in many scientific disciplines to model the dynamics arising from interactions described by reactions between molecules, individuals, or species. This study provides an overview of how Chemical Organization Theory (COT) can be used to analyze such systems by identifying all potentially persistent species solely from the underlying reaction network, without the need for simulations or even knowledge of reaction constants or kinetic laws. Two minimalist examples with only three resp. four species are used to introduce all fundamental definitions including a new, naturally arising concept of persistence, and to illustrate the fore-mentioned technique without mathematical details such as proofs. Thereby, COT is shown to provide measures to analyze, compare, and construct very complex systems on an abstract level and thus to complement other powerful techniques for the analysis of complex systems such as deficiency, RAF theory, elementary modes, graph theory, Lyapunov functions, and bifurcation theory.","PeriodicalId":51115,"journal":{"name":"Match-Communications in Mathematical and in Computer Chemistry","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82238236","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Sombor Index of c-Cyclic Chemical Graphs c-循环化学图的Sombor指数

IF 2.6 2区化学

Match-Communications in Mathematical and in Computer Chemistry Pub Date : 2023-04-01 DOI: 10.46793/match.90-2.495l

Hechao Liu, L. You, Yufei Huang

引用次数: 1

Resonance Graphs and a Binary Coding of Perfect Matchings of Outerplane Bipartite Graphs 共振图与外平面二部图完美匹配的二进制编码

IF 2.6 2区化学

Match-Communications in Mathematical and in Computer Chemistry Pub Date : 2023-04-01 DOI: 10.46793/match.90-2.453b

S. Brezovnik, Niko Tratnik, Petra Žigert Pleteršek

引用次数: 2

Protein Sequence Comparison Method Based on 3-ary Huffman Coding 基于3-ary Huffman编码的蛋白质序列比较方法

IF 2.6 2区化学

Match-Communications in Mathematical and in Computer Chemistry Pub Date : 2023-04-01 DOI: 10.46793/match.90-2.357q

Zhaohui Qi, Yingqiang Ning, Yinmei Huang

引用次数: 0