{"title":"Issue Information ‐ Table of Content","authors":"","doi":"10.1002/prot.25926","DOIUrl":"https://doi.org/10.1002/prot.25926","url":null,"abstract":"","PeriodicalId":20789,"journal":{"name":"Proteins: Structure","volume":"60 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80861470","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
New tyrosinases with putative action against contaminants of emerging concern Marcus V. X. Senra, Ana Lúcia Fonseca Novel antimicrobial anionic cecropins from the spruce budworm feature a poly-L-aspartic acid C-terminus Halim Maaroufi, Marianne Potvin, Michel Cusson, Roger C. Levesque Comparative Protein Structure Network Analysis on 3CLpro from SARS-CoV-1 and SARS-CoV-2 Surabhi Lata, Mohd. Akif Characterization of the multidrug efflux transporter styMdtMfrom Salmonella enterica serovar Typhi Aqsa Shaheen, Fouzia Ismat, Mazhar Iqbal, Abdul Haque, Zaheer Ul-Haq, Osman Mirza, Rita De Zorzi, Thomas Walz, Moazur Rahman Fungal Ice2p is in the same superfamily as SERINCs, restriction factors for HIV and other viruses Ganiyu O. Alli-Balogun, Tim P. Levine Conformation of Myelin Basic Protein Bound to Phosphatidylinositol Membrane Characterized by Vacuum-Ultraviolet Circular-Dichroism Spectroscopy and Molecular-Dynamics Simulations Munehiro Kumashiro, Yudai Izumi, Koichi Matsuo IGPRED: Combination of Convolutional Neural and Graph Convolutional Networks for Protein Secondary Structure Prediction Yasin Görmez, Mostafa Sabzekar, Zafer Aydin A Novel Measure to Analyze Protein Structures: Aspect Ratio in Protein Alpha Shapes Elife Z. Bagci, Fatma Senguler-Ciftci, Unver Ciftci, Ayhan Demir
Marcus V. X. Senra, Ana Lúcia Fonseca云云budworm的新型抗菌阴离子天门冬氨酸具有聚l -天冬氨酸c端Halim Maaroufi, Marianne Potvin, Michel Cusson, Roger C. Levesque在SARS-CoV-1和SARS-CoV-2中3CLpro的比较蛋白结构网络分析伤寒沙门氏菌血清型Aqsa Shaheen, Fouzia Ismat, Mazhar Iqbal, Abdul Haque, Zaheer Ul-Haq, Osman Mirza, Rita De Zorzi, Thomas Walz, Moazur Rahman真菌Ice2p与SERINCs、HIV和其他病毒的限制性因子属于同一个超家族。Munehiro Kumashiro, Yudai Izumi, Koichi Matsuo IGPRED:结合卷积神经网络和图卷积网络的蛋白质二级结构预测Yasin Görmez, Mostafa Sabzekar, Zafer Aydin蛋白质结构分析的新方法Elife Z. Bagci, Fatma senger -Ciftci, Unver Ciftci, Ayhan Demir
{"title":"Issue Information ‐ Forthcoming","authors":"Marcus V. X. Senra","doi":"10.1002/prot.25927","DOIUrl":"https://doi.org/10.1002/prot.25927","url":null,"abstract":"New tyrosinases with putative action against contaminants of emerging concern Marcus V. X. Senra, Ana Lúcia Fonseca Novel antimicrobial anionic cecropins from the spruce budworm feature a poly-L-aspartic acid C-terminus Halim Maaroufi, Marianne Potvin, Michel Cusson, Roger C. Levesque Comparative Protein Structure Network Analysis on 3CLpro from SARS-CoV-1 and SARS-CoV-2 Surabhi Lata, Mohd. Akif Characterization of the multidrug efflux transporter styMdtMfrom Salmonella enterica serovar Typhi Aqsa Shaheen, Fouzia Ismat, Mazhar Iqbal, Abdul Haque, Zaheer Ul-Haq, Osman Mirza, Rita De Zorzi, Thomas Walz, Moazur Rahman Fungal Ice2p is in the same superfamily as SERINCs, restriction factors for HIV and other viruses Ganiyu O. Alli-Balogun, Tim P. Levine Conformation of Myelin Basic Protein Bound to Phosphatidylinositol Membrane Characterized by Vacuum-Ultraviolet Circular-Dichroism Spectroscopy and Molecular-Dynamics Simulations Munehiro Kumashiro, Yudai Izumi, Koichi Matsuo IGPRED: Combination of Convolutional Neural and Graph Convolutional Networks for Protein Secondary Structure Prediction Yasin Görmez, Mostafa Sabzekar, Zafer Aydin A Novel Measure to Analyze Protein Structures: Aspect Ratio in Protein Alpha Shapes Elife Z. Bagci, Fatma Senguler-Ciftci, Unver Ciftci, Ayhan Demir","PeriodicalId":20789,"journal":{"name":"Proteins: Structure","volume":"30 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81440881","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Issue Information ‐ Table of Content","authors":"","doi":"10.1002/prot.25922","DOIUrl":"https://doi.org/10.1002/prot.25922","url":null,"abstract":"","PeriodicalId":20789,"journal":{"name":"Proteins: Structure","volume":"40 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78942018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Issue Information ‐ Table of Content","authors":"","doi":"10.1002/prot.25918","DOIUrl":"https://doi.org/10.1002/prot.25918","url":null,"abstract":"","PeriodicalId":20789,"journal":{"name":"Proteins: Structure","volume":"48 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73564940","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ligand‐induced transition in conformations of vicinal cysteine disulfides in proteins K Kasi Amarnath Reddy, Muddagoni Jayashree, Panchada Ch V Govindu, Konkallu Hanumae Gowd Deep learning pan‐specific model for interpretable MHC‐I peptide binding prediction with improved attention mechanism Jing Jin, Zhonghao Liu, Alireza Nasiri, Yuxin Cui, Stephen Louis, Ansi Zhang, Yong Zhao, Jianjun Hu Characterizing the function of domain linkers in regulating the dynamics of multi‐domain fusion proteins by microsecond molecular dynamics simulations and artificial intelligence Bo Wang, Zhaoqian Su, Yinghao Wu Mask Blast With A New Chemical Logic Of Amino Acids For Improved Protein Function Prediction Amita Pathak, Toran Roy, Avinash Edubilli, B. Jayaram Exploring the structure and dynamics of proteins in soil organic matter Mathias Gotsmy, Yerko Escalona, Chris Oostenbrink, Drazen Petrov Conformational Diversity Defines Substrate Specificity of Thymidylate/Uridylate Kinase from Candida albicans Kaustubh Sinha, Gordon S. Rule Citius, Altius, Fortius J. Lange, G. Vriend Purification, characterization, and crystal structure of YhdA‐type azoreductase from Bacillus velezensis Amit Bafana, Farha Khan, Kaza Suguna
K Kasi amarath Reddy, Muddagoni Jayashree, Panchada Ch V Govindu, Konkallu Hanumae god .基于改进注意机制的MHC - I肽结合预测深度学习泛特异性模型胡建军，王波，苏钊前，吴颖好，等。利用氨基酸化学逻辑改进蛋白质功能预测。Amita Pathak, Toran Roy, Avinash Edubilli, B. Jayaram研究土壤有机质中蛋白质的结构和动态Kaustubh Sinha, Gordon S. Rule Citius, Altius, Fortius J. Lange, G. vfriend来自velezensis Amit Bafana, Farha Khan, Kaza Suguna的YhdA型偶氮还原酶的纯化、表征和晶体结构
{"title":"Issue Information ‐ Forthcoming","authors":"Muddagoni Jayashree, Yerko Escalona","doi":"10.1002/prot.25919","DOIUrl":"https://doi.org/10.1002/prot.25919","url":null,"abstract":"Ligand‐induced transition in conformations of vicinal cysteine disulfides in proteins K Kasi Amarnath Reddy, Muddagoni Jayashree, Panchada Ch V Govindu, Konkallu Hanumae Gowd Deep learning pan‐specific model for interpretable MHC‐I peptide binding prediction with improved attention mechanism Jing Jin, Zhonghao Liu, Alireza Nasiri, Yuxin Cui, Stephen Louis, Ansi Zhang, Yong Zhao, Jianjun Hu Characterizing the function of domain linkers in regulating the dynamics of multi‐domain fusion proteins by microsecond molecular dynamics simulations and artificial intelligence Bo Wang, Zhaoqian Su, Yinghao Wu Mask Blast With A New Chemical Logic Of Amino Acids For Improved Protein Function Prediction Amita Pathak, Toran Roy, Avinash Edubilli, B. Jayaram Exploring the structure and dynamics of proteins in soil organic matter Mathias Gotsmy, Yerko Escalona, Chris Oostenbrink, Drazen Petrov Conformational Diversity Defines Substrate Specificity of Thymidylate/Uridylate Kinase from Candida albicans Kaustubh Sinha, Gordon S. Rule Citius, Altius, Fortius J. Lange, G. Vriend Purification, characterization, and crystal structure of YhdA‐type azoreductase from Bacillus velezensis Amit Bafana, Farha Khan, Kaza Suguna","PeriodicalId":20789,"journal":{"name":"Proteins: Structure","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73448557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Issue Information ‐ Table of Content","authors":"","doi":"10.1002/prot.25914","DOIUrl":"https://doi.org/10.1002/prot.25914","url":null,"abstract":"","PeriodicalId":20789,"journal":{"name":"Proteins: Structure","volume":"37 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84725893","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Daisuke Nakajima, Reza Kamali, J. Plowman, Rachel E. Miller, Anita J Grosvenor, D. Harland
Potential of Mean Force and Umbrella Sampling Simulation for the Transport of 5‐Oxazolidinone in Heterotetrameric Sarcosine Oxidase Shigetaka Yoneda, Takami Saito, Daisuke Nakajima, Go Watanabe Investigation of the aquaporin‐2 gating mechanism with molecular dynamics simulations Hooman Hadidi, Reza Kamali, Alireza Binesh Investigating the folding mechanism of the N‐terminal domain of ribosomal protein L9 Haozhe Zhang, Haomiao Zhang, Changjun Chen A detailed mapping of the readily accessible disulfide bonds in the cortex of wool fibers Jeffrey E. Plowman, Rachel E. Miller, Ancy Thomas, Anita J. Grosvenor, Duane P. Harland, Santanu Deb‐Choudhury Oxidation shuts down an auto‐inhibitory mechanism of von Willebrand factor Rachel Tsai, Gianluca Interlandi β‐sheet breakers with consecutive phenylalanines: insights into mechanism of dissolution of β‐amyloid fibrils Adam Jarmuła, Jan Ludwiczak, Dariusz Stępkowski A survey of human histone H1 subtypes interaction networks: implications for histones H1 functioning Andrzej Kowalski Ligand‐induced transition in conformations of vicinal cysteine disulfides in proteins K Kasi Amarnath Reddy, Muddagoni Jayashree, Panchada Ch V Govindu, Konkallu Hanumae Gowd
Shigetaka Yoneda, Takami Saito, Daisuke Nakajima, Go Watanabe用分子动力学模拟研究水通道蛋白2的门控机制Hooman Hadidi, Reza Kamali, Alireza Binesh研究核糖体蛋白L9 N端结构域的折叠机制张浩泽，张浩茂，Jeffrey E. Plowman, Rachel E. Miller, Ancy Thomas, Anita J. Grosvenor, Duane P. Harland, Santanu Deb - Choudhury氧化关闭von Willebrand因子的自抑制机制人类组蛋白H1亚型相互作用网络的调查:对组蛋白H1功能的影响。Andrzej Kowalski配体诱导的蛋白质中邻近半胱氨酸二硫化合物构象的转变
{"title":"Issue Information ‐ Forthcoming","authors":"Daisuke Nakajima, Reza Kamali, J. Plowman, Rachel E. Miller, Anita J Grosvenor, D. Harland","doi":"10.1002/prot.25915","DOIUrl":"https://doi.org/10.1002/prot.25915","url":null,"abstract":"Potential of Mean Force and Umbrella Sampling Simulation for the Transport of 5‐Oxazolidinone in Heterotetrameric Sarcosine Oxidase Shigetaka Yoneda, Takami Saito, Daisuke Nakajima, Go Watanabe Investigation of the aquaporin‐2 gating mechanism with molecular dynamics simulations Hooman Hadidi, Reza Kamali, Alireza Binesh Investigating the folding mechanism of the N‐terminal domain of ribosomal protein L9 Haozhe Zhang, Haomiao Zhang, Changjun Chen A detailed mapping of the readily accessible disulfide bonds in the cortex of wool fibers Jeffrey E. Plowman, Rachel E. Miller, Ancy Thomas, Anita J. Grosvenor, Duane P. Harland, Santanu Deb‐Choudhury Oxidation shuts down an auto‐inhibitory mechanism of von Willebrand factor Rachel Tsai, Gianluca Interlandi β‐sheet breakers with consecutive phenylalanines: insights into mechanism of dissolution of β‐amyloid fibrils Adam Jarmuła, Jan Ludwiczak, Dariusz Stępkowski A survey of human histone H1 subtypes interaction networks: implications for histones H1 functioning Andrzej Kowalski Ligand‐induced transition in conformations of vicinal cysteine disulfides in proteins K Kasi Amarnath Reddy, Muddagoni Jayashree, Panchada Ch V Govindu, Konkallu Hanumae Gowd","PeriodicalId":20789,"journal":{"name":"Proteins: Structure","volume":"16 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80847939","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The structure of a protein plays a pivotal role in determining its function. Often, the protein surface's shape and curvature dictate its nature of interaction with other proteins and biomolecules. However, marked by corrugations and roughness, a protein's surface representation poses significant challenges for its curvature‐based characterization. In the present study, we employ unsupervised machine learning to segment the protein surface into patches. To measure the surface curvature of a patch, we present an algebraic sphere fitting method that is fast, accurate, and robust. Moreover, we use local curvatures to show the existence of “shape complementarity” in protein–protein, antigen–antibody, and protein‐ligand interfaces. We believe that the current approach could help understand the relationship between protein structure and its biological function and can be used to find binding partners of a given protein.
{"title":"Capturing surface complementarity in proteins using unsupervised learning and robust curvature measure","authors":"Abhijit Gupta, A. Mukherjee","doi":"10.1002/prot.26345","DOIUrl":"https://doi.org/10.1002/prot.26345","url":null,"abstract":"The structure of a protein plays a pivotal role in determining its function. Often, the protein surface's shape and curvature dictate its nature of interaction with other proteins and biomolecules. However, marked by corrugations and roughness, a protein's surface representation poses significant challenges for its curvature‐based characterization. In the present study, we employ unsupervised machine learning to segment the protein surface into patches. To measure the surface curvature of a patch, we present an algebraic sphere fitting method that is fast, accurate, and robust. Moreover, we use local curvatures to show the existence of “shape complementarity” in protein–protein, antigen–antibody, and protein‐ligand interfaces. We believe that the current approach could help understand the relationship between protein structure and its biological function and can be used to find binding partners of a given protein.","PeriodicalId":20789,"journal":{"name":"Proteins: Structure","volume":"20 1","pages":"1669 - 1683"},"PeriodicalIF":0.0,"publicationDate":"2021-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81998046","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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