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Computational Analysis and Rational Design of N-substituting Perturbation on the Affinity and Specificity of Pediatric Fyn SH3–Peptoid Interaction n -取代扰动对儿童Fyn SH3-Peptoid相互作用亲和力和特异性的计算分析和合理设计
IF 2.2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2023-06-20 DOI: 10.1142/s2737416523500394
Qin Liu, Jie Wang, Lin Shi, Xiang Shao
{"title":"Computational Analysis and Rational Design of N-substituting Perturbation on the Affinity and Specificity of Pediatric Fyn SH3–Peptoid Interaction","authors":"Qin Liu, Jie Wang, Lin Shi, Xiang Shao","doi":"10.1142/s2737416523500394","DOIUrl":"https://doi.org/10.1142/s2737416523500394","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44854465","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
Closed-loop deep brain stimulation using a type of fixed-time sliding mode controller for avoiding epileptiform discharge in a human cortical model 使用一种固定时间滑模控制器的闭环脑深部刺激以避免人类皮层模型中的癫痫样放电
IF 2.2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2023-06-20 DOI: 10.1142/s2737416523500382
S. Mohammad‐Ali‐Nezhad, Samira Rezvani-Ardakani, R. Ghasemi
{"title":"Closed-loop deep brain stimulation using a type of fixed-time sliding mode controller for avoiding epileptiform discharge in a human cortical model","authors":"S. Mohammad‐Ali‐Nezhad, Samira Rezvani-Ardakani, R. Ghasemi","doi":"10.1142/s2737416523500382","DOIUrl":"https://doi.org/10.1142/s2737416523500382","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2023-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44932735","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
Modeling of Conjugated Core-Based Non-Fullerene Acceptor Materials for Organic Photovoltaic Applications 有机光伏应用中共轭核基非富勒烯受体材料的建模
IF 2.2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2023-06-16 DOI: 10.1142/s2737416523500370
Muhammad Adnan, M. Faisal, Riaz Hussain, Muhammad Usman Khan, Junaid Yaqoob, Fakhar Hussain, S. A. Siddique, Umar Farooq, C. Cho, Jongchul Lim
{"title":"Modeling of Conjugated Core-Based Non-Fullerene Acceptor Materials for Organic Photovoltaic Applications","authors":"Muhammad Adnan, M. Faisal, Riaz Hussain, Muhammad Usman Khan, Junaid Yaqoob, Fakhar Hussain, S. A. Siddique, Umar Farooq, C. Cho, Jongchul Lim","doi":"10.1142/s2737416523500370","DOIUrl":"https://doi.org/10.1142/s2737416523500370","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2023-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42352617","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
Molecular dynamics studies of mixtures of a deep eutectic solvent and cosolvents 深共晶溶剂和共溶剂混合物的分子动力学研究
IF 2.2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2023-06-09 DOI: 10.1142/s2737416523500369
D. Panda, B. L. Bhargava
{"title":"Molecular dynamics studies of mixtures of a deep eutectic solvent and cosolvents","authors":"D. Panda, B. L. Bhargava","doi":"10.1142/s2737416523500369","DOIUrl":"https://doi.org/10.1142/s2737416523500369","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2023-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42901111","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 of bridge-driven engineering of non-fullerene based acceptors for efficacious organic solar cell applications 用于有效有机太阳能电池应用的非富勒烯基受体桥驱动工程的DFT研究
IF 2.2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2023-06-02 DOI: 10.1142/s2737416523420036
A. R. Ayub, Umer Yaqoob, Sidra Rafiq, Salba Arshad, Muhammad Umar Dad, Haiyang Li
{"title":"A DFT study of bridge-driven engineering of non-fullerene based acceptors for efficacious organic solar cell applications","authors":"A. R. Ayub, Umer Yaqoob, Sidra Rafiq, Salba Arshad, Muhammad Umar Dad, Haiyang Li","doi":"10.1142/s2737416523420036","DOIUrl":"https://doi.org/10.1142/s2737416523420036","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2023-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48464391","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
Assessments of Variational Autoencoder in Protein Conformation Exploration. 变分自编码器在蛋白质构象探测中的应用评价
IF 2.2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2023-06-01 Epub Date: 2023-03-27 DOI: 10.1142/s2737416523500217
Sian Xiao, Zilin Song, Hao Tian, Peng Tao
{"title":"Assessments of Variational Autoencoder in Protein Conformation Exploration.","authors":"Sian Xiao, Zilin Song, Hao Tian, Peng Tao","doi":"10.1142/s2737416523500217","DOIUrl":"10.1142/s2737416523500217","url":null,"abstract":"<p><p>Molecular dynamics (MD) simulations have been extensively used to study protein dynamics and subsequently functions. However, MD simulations are often insufficient to explore adequate conformational space for protein functions within reachable timescales. Accordingly, many enhanced sampling methods, including variational autoencoder (VAE) based methods, have been developed to address this issue. The purpose of this study is to evaluate the feasibility of using VAE to assist in the exploration of protein conformational landscapes. Using three modeling systems, we showed that VAE could capture high-level hidden information which distinguishes protein conformations. These models could also be used to generate new physically plausible protein conformations for direct sampling in favorable conformational spaces. We also found that VAE worked better in interpolation than extrapolation and increasing latent space dimension could lead to a trade-off between performances and complexities.</p>","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11138204/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48657145","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
In Silico Studies, Design and Synthesis of Novel Fused Pyrimidine Derivatives as A DNA Gyrase Inhibitor and Antibacterial Activity Against Quinolone Resistant Escherichia Coli 新型融合嘧啶衍生物DNA回转酶抑制剂的设计与合成及其对耐喹诺酮类大肠杆菌的抑菌活性
IF 2.2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2023-05-26 DOI: 10.1142/s2737416523500357
R. Bhandare, N. Helina, A. Subramani, Ramalakshmi Natarajan, Suraj N. Mali, A. Shaik
{"title":"In Silico Studies, Design and Synthesis of Novel Fused Pyrimidine Derivatives as A DNA Gyrase Inhibitor and Antibacterial Activity Against Quinolone Resistant Escherichia Coli","authors":"R. Bhandare, N. Helina, A. Subramani, Ramalakshmi Natarajan, Suraj N. Mali, A. Shaik","doi":"10.1142/s2737416523500357","DOIUrl":"https://doi.org/10.1142/s2737416523500357","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2023-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42275963","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
Computational insight into electronic, optical and photophysical properties of small compounds for solar cell applications 对太阳能电池应用中小化合物的电子、光学和光物理性质的计算洞察力
IF 2.2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2023-05-26 DOI: 10.1142/s2737416523420024
A. R. Chaudhry, Yahia A. H. Obaidat, S. Muhammad, Saifedin Y. DaifAllah, B. Ul Haq
{"title":"Computational insight into electronic, optical and photophysical properties of small compounds for solar cell applications","authors":"A. R. Chaudhry, Yahia A. H. Obaidat, S. Muhammad, Saifedin Y. DaifAllah, B. Ul Haq","doi":"10.1142/s2737416523420024","DOIUrl":"https://doi.org/10.1142/s2737416523420024","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2023-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"63853746","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
Exploring key proteins, pathways and oxygen usage bias of proteins and metabolites in melanoma 探讨黑色素瘤中蛋白质和代谢产物的关键蛋白质、途径和氧使用偏差
IF 2.2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2023-05-22 DOI: 10.1142/s2737416523500345
Mancong Zhang, Chengxu Zhu, Zeyu Luo, Junhao Liu, Muhammad Tahir Khan, Yawen Sun, Dongqing Wei, Yu-Juan Zhang
{"title":"Exploring key proteins, pathways and oxygen usage bias of proteins and metabolites in melanoma","authors":"Mancong Zhang, Chengxu Zhu, Zeyu Luo, Junhao Liu, Muhammad Tahir Khan, Yawen Sun, Dongqing Wei, Yu-Juan Zhang","doi":"10.1142/s2737416523500345","DOIUrl":"https://doi.org/10.1142/s2737416523500345","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2023-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44490105","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
Role of Aromatic Heterocyclic Core-Based Materials as Donors for Organic and as Hole Transport Materials for Perovskites Solar cells 芳香杂环核基材料作为钙钛矿太阳能电池有机供体和空穴输运材料的作用
IF 2.2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2023-05-12 DOI: 10.1142/s2737416523420012
Muhammad Adnan, Qandeel Fatima, Zobia Irshad, Riaz Hussain, Junaid Yaqoob, Muhammad Usman Khan, Nooruddin Ansari, S. A. Siddique, Jongchul Lim
{"title":"Role of Aromatic Heterocyclic Core-Based Materials as Donors for Organic and as Hole Transport Materials for Perovskites Solar cells","authors":"Muhammad Adnan, Qandeel Fatima, Zobia Irshad, Riaz Hussain, Junaid Yaqoob, Muhammad Usman Khan, Nooruddin Ansari, S. A. Siddique, Jongchul Lim","doi":"10.1142/s2737416523420012","DOIUrl":"https://doi.org/10.1142/s2737416523420012","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2023-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43438357","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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