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Biomolecular Simulations in Structure-Based Drug Discovery最新文献

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Molecular Dynamics-Based Approaches Describing Protein Binding 基于分子动力学的蛋白质结合描述方法
Biomolecular Simulations in Structure-Based Drug Discovery Pub Date : 2018-12-21 DOI: 10.1002/9783527806836.CH2
A. Spitaleri, W. Rocchia
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引用次数: 3
Monte Carlo Techniques for Drug Design: The Success Case of PELE 蒙特卡罗技术用于药物设计:PELE的成功案例
Biomolecular Simulations in Structure-Based Drug Discovery Pub Date : 2018-12-21 DOI: 10.1002/9783527806836.CH5
J. Gilabert, D. Lecina, Jorge Estrada, V. Guallar
{"title":"Monte Carlo Techniques for Drug Design: The Success Case of PELE","authors":"J. Gilabert, D. Lecina, Jorge Estrada, V. Guallar","doi":"10.1002/9783527806836.CH5","DOIUrl":"https://doi.org/10.1002/9783527806836.CH5","url":null,"abstract":"This chapter summarizes the most representative software packages that readily allow running Monte Carlo (MC) simulations in relevant scenarios for drug design. It explores in detail the Protein Energy Landscape Exploration (PELE) program, providing first the main characteristics of the technique, followed by an analysis of the different application studies in mapping protein‐ligand interactions. The ligand, formed by a rigid core and a set of rotatable side chains, is perturbed by translating and rotating it. PELE creates a list of perturbation poses, and then chooses the one with the lowest system energy. PELE was originally designed to map ligand migration pathways: its first applications aimed at finding exit pathways starting from ligand‐bound crystallographic structures. Additional applied studies have centered on modeling enzymatic mechanisms and engineering; the same techniques applied in mapping protein‐drug interactions can be used in the study of substrate recognition by enzymes.","PeriodicalId":427626,"journal":{"name":"Biomolecular Simulations in Structure-Based Drug Discovery","volume":"391 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115915066","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}
引用次数: 16
Structure and Stability of Amyloid Protofibrils of Polyglutamine and Polyasparagine from Molecular Dynamics Simulations 基于分子动力学模拟的聚谷氨酰胺和聚天冬酰胺淀粉样原纤维的结构和稳定性
Biomolecular Simulations in Structure-Based Drug Discovery Pub Date : 2018-12-21 DOI: 10.1002/9783527806836.CH12
V. H. Man, Y. Zhang, C. Roland, C. Sagui
{"title":"Structure and Stability of Amyloid Protofibrils of Polyglutamine and Polyasparagine from Molecular Dynamics Simulations","authors":"V. H. Man, Y. Zhang, C. Roland, C. Sagui","doi":"10.1002/9783527806836.CH12","DOIUrl":"https://doi.org/10.1002/9783527806836.CH12","url":null,"abstract":"","PeriodicalId":427626,"journal":{"name":"Biomolecular Simulations in Structure-Based Drug Discovery","volume":"89 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123759341","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}
引用次数: 1
From Computers to Bedside: Computational Chemistry Contributing to FDA Approval 从计算机到床边:计算化学有助于FDA批准
Biomolecular Simulations in Structure-Based Drug Discovery Pub Date : 2018-12-21 DOI: 10.1002/9783527806836.CH7
C. Athanasiou, Z. Cournia
{"title":"From Computers to Bedside: Computational Chemistry Contributing to FDA Approval","authors":"C. Athanasiou, Z. Cournia","doi":"10.1002/9783527806836.CH7","DOIUrl":"https://doi.org/10.1002/9783527806836.CH7","url":null,"abstract":"","PeriodicalId":427626,"journal":{"name":"Biomolecular Simulations in Structure-Based Drug Discovery","volume":"64 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127943693","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}
引用次数: 5
Ion Channel Simulations 离子通道模拟
Biomolecular Simulations in Structure-Based Drug Discovery Pub Date : 2018-12-21 DOI: 10.1002/9783527806836.CH10
S. Pandey, D. Bonhenry, R. Ettrich
{"title":"Ion Channel Simulations","authors":"S. Pandey, D. Bonhenry, R. Ettrich","doi":"10.1002/9783527806836.CH10","DOIUrl":"https://doi.org/10.1002/9783527806836.CH10","url":null,"abstract":"","PeriodicalId":427626,"journal":{"name":"Biomolecular Simulations in Structure-Based Drug Discovery","volume":"69 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131617930","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}
引用次数: 0
Understanding Allostery to Design New Drugs 理解变构以设计新药
Biomolecular Simulations in Structure-Based Drug Discovery Pub Date : 2018-12-21 DOI: 10.1002/9783527806836.CH11
G. Morra, G. Colombo
{"title":"Understanding Allostery to Design New Drugs","authors":"G. Morra, G. Colombo","doi":"10.1002/9783527806836.CH11","DOIUrl":"https://doi.org/10.1002/9783527806836.CH11","url":null,"abstract":"","PeriodicalId":427626,"journal":{"name":"Biomolecular Simulations in Structure-Based Drug Discovery","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134628912","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}
引用次数: 0
Using Biomolecular Simulations to Target Cdc34 in Cancer 利用生物分子模拟靶向Cdc34治疗癌症
Biomolecular Simulations in Structure-Based Drug Discovery Pub Date : 2018-12-21 DOI: 10.1002/9783527806836.CH13
Miriam Di Marco, M. Lambrughi, Elena Papaleo
{"title":"Using Biomolecular Simulations to Target Cdc34 in Cancer","authors":"Miriam Di Marco, M. Lambrughi, Elena Papaleo","doi":"10.1002/9783527806836.CH13","DOIUrl":"https://doi.org/10.1002/9783527806836.CH13","url":null,"abstract":"","PeriodicalId":427626,"journal":{"name":"Biomolecular Simulations in Structure-Based Drug Discovery","volume":"196 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116367360","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}
引用次数: 0
Modeling Ligand-Target Binding with Enhanced Sampling Simulations 基于增强采样模拟的配体-靶结合模型
Biomolecular Simulations in Structure-Based Drug Discovery Pub Date : 2018-12-21 DOI: 10.1002/9783527806836.CH3
Federico Comitani, F. Gervasio
{"title":"Modeling Ligand-Target Binding with Enhanced Sampling Simulations","authors":"Federico Comitani, F. Gervasio","doi":"10.1002/9783527806836.CH3","DOIUrl":"https://doi.org/10.1002/9783527806836.CH3","url":null,"abstract":"","PeriodicalId":427626,"journal":{"name":"Biomolecular Simulations in Structure-Based Drug Discovery","volume":"50 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130680762","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}
引用次数: 1
Understanding the Structure and Dynamics of Peptides and Proteins Through the Lens of Network Science 从网络科学的角度理解多肽和蛋白质的结构和动力学
Biomolecular Simulations in Structure-Based Drug Discovery Pub Date : 2018-12-21 DOI: 10.1002/9783527806836.CH6
Mathieu Fossépré, Mathieu Fossépré, L. Leherte, A. Laaksonen, A. Laaksonen, Daneil P. Vercauteren
{"title":"Understanding the Structure and Dynamics of Peptides and Proteins Through the Lens of Network Science","authors":"Mathieu Fossépré, Mathieu Fossépré, L. Leherte, A. Laaksonen, A. Laaksonen, Daneil P. Vercauteren","doi":"10.1002/9783527806836.CH6","DOIUrl":"https://doi.org/10.1002/9783527806836.CH6","url":null,"abstract":"Understanding the Structure and Dynamics of Peptides and Proteins Through the Lens of Network Science","PeriodicalId":427626,"journal":{"name":"Biomolecular Simulations in Structure-Based Drug Discovery","volume":"12 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130037941","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}
引用次数: 3
Predictive Power of Biomolecular Simulations 生物分子模拟的预测能力
Biomolecular Simulations in Structure-Based Drug Discovery Pub Date : 2018-12-21 DOI: 10.1002/9783527806836.CH1
V. Spiwok
{"title":"Predictive Power of Biomolecular Simulations","authors":"V. Spiwok","doi":"10.1002/9783527806836.CH1","DOIUrl":"https://doi.org/10.1002/9783527806836.CH1","url":null,"abstract":"","PeriodicalId":427626,"journal":{"name":"Biomolecular Simulations in Structure-Based Drug Discovery","volume":"64 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124769483","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}
引用次数: 0
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