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Persistent topological Laplacian analysis of SARS-CoV-2 variants. 严重急性呼吸系统综合征冠状病毒2型变异株的持久拓扑拉普拉斯分析。
IF 2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2023-08-01 Epub Date: 2023-06-08 DOI: 10.1142/s2737416523500278
Xiaoqi Wei, Jiahui Chen, Guo-Wei Wei
{"title":"Persistent topological Laplacian analysis of SARS-CoV-2 variants.","authors":"Xiaoqi Wei, Jiahui Chen, Guo-Wei Wei","doi":"10.1142/s2737416523500278","DOIUrl":"10.1142/s2737416523500278","url":null,"abstract":"<p><p>Topological data analysis (TDA) is an emerging field in mathematics and data science. Its central technique, persistent homology, has had tremendous success in many science and engineering disciplines. However, persistent homology has limitations, including its inability to handle heterogeneous information, such as multiple types of geometric objects; being qualitative rather than quantitative, e.g., counting a 5-member ring the same as a 6-member ring, and a failure to describe non-topological changes, such as homotopic changes in protein-protein binding. Persistent topological Laplacians (PTLs), such as persistent Laplacian and persistent sheaf Laplacian, were proposed to overcome the limitations of persistent homology. In this work, we examine the modeling and analysis power of PTLs in the study of the protein structures of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike receptor binding domain (RBD). First, we employ PTLs to study how the RBD mutation-induced structural changes of RBD-angiotensin-converting enzyme 2 (ACE2) binding complexes are captured in the changes of spectra of the PTLs among SARS-CoV-2 variants. Additionally, we use PTLs to analyze the binding of RBD and ACE2-induced structural changes of various SARS-CoV-2 variants. Finally, we explore the impacts of computationally generated RBD structures on a topological deep learning paradigm and predictions of deep mutational scanning datasets for the SARS-CoV-2 Omicron BA.2 variant. Our results indicate that PTLs have advantages over persistent homology in analyzing protein structural changes and provide a powerful new TDA tool for data science.</p>","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10569362/pdf/nihms-1888545.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41202808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
PKAD-2: New entries and expansion of functionalities of the database of experimentally measured pKa's of proteins. PKAD-2:实验测量蛋白质pKa的数据库的新条目和功能扩展。
IF 2.2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2023-08-01 DOI: 10.1142/s2737416523500230
Nicolas Ancona, Ananta Bastola, Emil Alexov
{"title":"PKAD-2: New entries and expansion of functionalities of the database of experimentally measured pKa's of proteins.","authors":"Nicolas Ancona,&nbsp;Ananta Bastola,&nbsp;Emil Alexov","doi":"10.1142/s2737416523500230","DOIUrl":"https://doi.org/10.1142/s2737416523500230","url":null,"abstract":"<p><p>Almost all biological reactions are pH dependent and understanding the origin of pH dependence requires knowledge of the pKa's of ionizable groups. Here we report a new edition of PKAD, the PKAD-2, which is a database of experimentally measured pKa's of proteins, both wild type and mutant proteins. The new additions include 117 wild type and 54 mutant pKa values, resulting in total 1742 experimentally measured pKa's. The new edition of PKAD-2 includes 8 new wild type and 12 new mutant proteins, resulting in total of 220 proteins. This new edition incorporates a visual 3D image of the highlighted residue of interest within the corresponding protein or protein complex. Hydrogen bonds were identified, counted, and implemented as a search feature. Other new search features include the number of neighboring residues <4A from the heaviest atom of the side chain of a given amino acid. Here, we present PKAD-2 with the intention to continuously incorporate novel features and current data with the goal to be used as benchmark for computational methods.</p>","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10373500/pdf/nihms-1915764.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10354730","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Synthesis, Characterization, Density Functional Theory, Monte Carlo, and Molecular Dynamics Simulations of [NI(II)(TPY)2] Metal Organic Framework and Congo Red Dye Application [NI(II)(TPY)2]金属有机骨架的合成、表征、密度泛函理论、蒙特卡罗和分子动力学模拟及刚果红染料的应用
IF 2.2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2023-07-28 DOI: 10.1142/s2737416523500448
M. D. Olawale, E. Akintemi, N. Ojo, A. Isaac, H. Su, J. Obaleye
{"title":"Synthesis, Characterization, Density Functional Theory, Monte Carlo, and Molecular Dynamics Simulations of [NI(II)(TPY)2] Metal Organic Framework and Congo Red Dye Application","authors":"M. D. Olawale, E. Akintemi, N. Ojo, A. Isaac, H. Su, J. Obaleye","doi":"10.1142/s2737416523500448","DOIUrl":"https://doi.org/10.1142/s2737416523500448","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2023-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48736938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Fine-Tuning of the Electronic and Optical Properties of Dodecabenzocoronene through Boron and Nitrogen Doping: A DFT Insight 硼和氮掺杂对十二苯二溴烯电子和光学性质的微调:一个DFT的见解
IF 2.2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2023-07-28 DOI: 10.1142/s273741652342005x
S. Sarfaraz, Ahmed Lakhani, Riaz Hussain, K. Ayub
{"title":"Fine-Tuning of the Electronic and Optical Properties of Dodecabenzocoronene through Boron and Nitrogen Doping: A DFT Insight","authors":"S. Sarfaraz, Ahmed Lakhani, Riaz Hussain, K. Ayub","doi":"10.1142/s273741652342005x","DOIUrl":"https://doi.org/10.1142/s273741652342005x","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2023-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47754378","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Erratum: Designing Potential Inhibitors of SARS-CoV-2 Mpro Using Deep Learning and Steered Molecular Dynamic Simulations 利用深度学习和定向分子动力学模拟设计SARS-CoV-2 Mpro的潜在抑制剂
IF 2.2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2023-07-25 DOI: 10.1142/s2737416523920023
N. M. Tam, L. Tran, Q. Vo, Minh Quan Pham, H. Phung
{"title":"Erratum: Designing Potential Inhibitors of SARS-CoV-2 Mpro Using Deep Learning and Steered Molecular Dynamic Simulations","authors":"N. M. Tam, L. Tran, Q. Vo, Minh Quan Pham, H. Phung","doi":"10.1142/s2737416523920023","DOIUrl":"https://doi.org/10.1142/s2737416523920023","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2023-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44424341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
A Multi-target Study of Natural Compounds in Preventing Neurodegenerative Disease Progression: A Computational Modeling Study 预防神经退行性疾病进展的天然化合物的多靶点研究:计算模型研究
IF 2.2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2023-07-21 DOI: 10.1142/s2737416523500436
Yuri Alves de Oliveira Só, MonicaA. Silva, A. S. Kiametis, C. Sette, M. L. Pereira Júnior, L. A. R. Júnior, R. Gargano
{"title":"A Multi-target Study of Natural Compounds in Preventing Neurodegenerative Disease Progression: A Computational Modeling Study","authors":"Yuri Alves de Oliveira Só, MonicaA. Silva, A. S. Kiametis, C. Sette, M. L. Pereira Júnior, L. A. R. Júnior, R. Gargano","doi":"10.1142/s2737416523500436","DOIUrl":"https://doi.org/10.1142/s2737416523500436","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2023-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45909266","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Influence of velocity slip and viscous dissipation on MHD heat transfer Fe3O4 - Ethylene Glycol Nanofluid flow over a shrinking sheet with thermal radiation 速度滑移和粘性耗散对热辐射收缩板上Fe3O4-乙二醇纳米流体MHD传热的影响
IF 2.2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2023-07-21 DOI: 10.1142/s2737416523500424
Y. Dharmendar Reddy, I. Mangamma
{"title":"Influence of velocity slip and viscous dissipation on MHD heat transfer Fe3O4 - Ethylene Glycol Nanofluid flow over a shrinking sheet with thermal radiation","authors":"Y. Dharmendar Reddy, I. Mangamma","doi":"10.1142/s2737416523500424","DOIUrl":"https://doi.org/10.1142/s2737416523500424","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2023-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48329201","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
A DFT study on the impact of saturated and conjugated side chains on the optoelectronic performance of Y-series non-fullerene acceptors 饱和和共轭侧链对Y系列非富勒烯受体光电性能影响的DFT研究
IF 2.2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2023-07-21 DOI: 10.1142/s2737416523420048
Fareeda Kalsoom, Umer Farooq, M. Salman, Riaz Hussain
{"title":"A DFT study on the impact of saturated and conjugated side chains on the optoelectronic performance of Y-series non-fullerene acceptors","authors":"Fareeda Kalsoom, Umer Farooq, M. Salman, Riaz Hussain","doi":"10.1142/s2737416523420048","DOIUrl":"https://doi.org/10.1142/s2737416523420048","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2023-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41337638","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Synthesis, In Silico, In Vitro and DFT Assessments of Substituted Imidazopyridine Derivatives as Potential Antimalarials Targeting Hemoglobin Degradation Pathway 取代咪唑吡啶衍生物作为靶向血红蛋白降解途径的潜在抗疟药物的合成、硅、体外和DFT评价
IF 2.2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2023-07-14 DOI: 10.1142/s2737416523500412
Oberdan Oliveira Ferreira, Suraj N. Mali, Bhagwat Jadhav, Samir Chtita, A. Kuznetsov, R. Bhandare, A. Shaik, Farhan Siddique, Akshay Yadav, Chin‐Hung Lai, J. Cruz, E. H. de Aguiar Andrade, S. Arvindekar, R. Jawarkar, M. D. de Oliveira
{"title":"Synthesis, In Silico, In Vitro and DFT Assessments of Substituted Imidazopyridine Derivatives as Potential Antimalarials Targeting Hemoglobin Degradation Pathway","authors":"Oberdan Oliveira Ferreira, Suraj N. Mali, Bhagwat Jadhav, Samir Chtita, A. Kuznetsov, R. Bhandare, A. Shaik, Farhan Siddique, Akshay Yadav, Chin‐Hung Lai, J. Cruz, E. H. de Aguiar Andrade, S. Arvindekar, R. Jawarkar, M. D. de Oliveira","doi":"10.1142/s2737416523500412","DOIUrl":"https://doi.org/10.1142/s2737416523500412","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2023-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45908851","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Electronic and NLO Performances of Benzohydrazide Derivatives: DFT Investigation and (RDG, AIM) Analysis 苯并肼衍生物的电子和NLO性能:DFT研究和(RDG, AIM)分析
IF 2.2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2023-06-30 DOI: 10.1142/s2737416523500400
N. Benhalima, B. Doumi, Oumria Kourat, Fatima Yahia Cherif, Nour El houda Daho, A. Chouaih, A. Sayede
{"title":"Electronic and NLO Performances of Benzohydrazide Derivatives: DFT Investigation and (RDG, AIM) Analysis","authors":"N. Benhalima, B. Doumi, Oumria Kourat, Fatima Yahia Cherif, Nour El houda Daho, A. Chouaih, A. Sayede","doi":"10.1142/s2737416523500400","DOIUrl":"https://doi.org/10.1142/s2737416523500400","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2023-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44790497","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
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