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Journal of Computational Biophysics and Chemistry最新文献

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PKAD-2: New entries and expansion of functionalities of the database of experimentally measured pKa's of proteins. PKAD-2：蛋白质实验测量 pKa 数据库的新条目和功能扩展。
IF 4.6 4区 化学 Q3 CHEMISTRY, MULTIDISCIPLINARY
Journal of Computational Biophysics and Chemistry
Pub Date : 2023-08-01 Epub Date: 2023-04-25 DOI: 10.1142/s2737416523500230
Nicolas Ancona, Ananta Bastola, Emil Alexov

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.

几乎所有生物反应都与 pH 值有关，而要了解 pH 值依赖性的起源，就必须了解可电离基团的 pKa。在此，我们报告了新版 PKAD，即 PKAD-2，这是一个通过实验测得的蛋白质 pKa 数据库，包括野生型蛋白质和突变型蛋白质。新增加的数据包括 117 个野生型和 54 个突变型 pKa 值，因此实验测量的 pKa 值总数为 1742 个。新版 PKAD-2 包括 8 个新的野生型蛋白质和 12 个新的突变型蛋白质，因此共有 220 个蛋白质。新版中加入了相应蛋白质或蛋白质复合物中感兴趣的高亮残基的可视化三维图像。氢键已被识别、计数并作为搜索功能使用。其他新的搜索功能包括邻近残基的数量
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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 Q3 CHEMISTRY, MULTIDISCIPLINARY
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
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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 Q3 CHEMISTRY, MULTIDISCIPLINARY
Journal of Computational Biophysics and Chemistry
Pub Date : 2023-07-28 DOI: 10.1142/s273741652342005x
S. Sarfaraz, Ahmed Lakhani, Riaz Hussain, K. Ayub
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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 Q3 CHEMISTRY, MULTIDISCIPLINARY
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":" ","pages":""},"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 Q3 CHEMISTRY, MULTIDISCIPLINARY
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
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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 Q3 CHEMISTRY, MULTIDISCIPLINARY
Journal of Computational Biophysics and Chemistry
Pub Date : 2023-07-21 DOI: 10.1142/s2737416523500424
Y. Dharmendar Reddy, I. Mangamma
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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 Q3 CHEMISTRY, MULTIDISCIPLINARY
Journal of Computational Biophysics and Chemistry
Pub Date : 2023-07-21 DOI: 10.1142/s2737416523420048
Fareeda Kalsoom, Umer Farooq, M. Salman, Riaz Hussain
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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 Q3 CHEMISTRY, MULTIDISCIPLINARY
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
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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 Q3 CHEMISTRY, MULTIDISCIPLINARY
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
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引用次数: 0
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 Q3 CHEMISTRY, MULTIDISCIPLINARY
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":" ","pages":""},"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
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