Pub Date : 2024-01-01Epub Date: 2024-10-21DOI: 10.4310/cis.241021221101
Zhiwei Ma, Abeeb Ajibade, Xiaoqin Zou
Molecular docking stands as a pivotal element in the realm of computer-aided drug design (CADD), consistently contributing to advancements in pharmaceutical research. In essence, it employs computer algorithms to identify the "best" match between two molecules, akin to solving intricate three-dimensional jigsaw puzzles. At a more stringent level, the molecular docking challenge entails predicting the accurate bound association state based on the atomic coordinates of two molecules. This process assumes particular significance in unraveling the mechanistic intricacies of physicochemical interactions at the atomic scale. Notably, the application of docking, especially in the context of protein-small molecule interactions, holds wide-ranging implications for structure-based drug design, given the prevalent use of small compounds as drug candidates. This study provides an overview of docking methodologies, delves into recent key developments, elucidates the physicochemical underpinnings of molecular recognition in protein-ligand interactions, and concludes by addressing the applications of docking in virtual screening, alongside current challenges within existing docking methods.
{"title":"Docking strategies for predicting protein-ligand interactions and their application to structure-based drug design.","authors":"Zhiwei Ma, Abeeb Ajibade, Xiaoqin Zou","doi":"10.4310/cis.241021221101","DOIUrl":"10.4310/cis.241021221101","url":null,"abstract":"<p><p>Molecular docking stands as a pivotal element in the realm of computer-aided drug design (CADD), consistently contributing to advancements in pharmaceutical research. In essence, it employs computer algorithms to identify the \"best\" match between two molecules, akin to solving intricate three-dimensional jigsaw puzzles. At a more stringent level, the molecular docking challenge entails predicting the accurate bound association state based on the atomic coordinates of two molecules. This process assumes particular significance in unraveling the mechanistic intricacies of physicochemical interactions at the atomic scale. Notably, the application of docking, especially in the context of protein-small molecule interactions, holds wide-ranging implications for structure-based drug design, given the prevalent use of small compounds as drug candidates. This study provides an overview of docking methodologies, delves into recent key developments, elucidates the physicochemical underpinnings of molecular recognition in protein-ligand interactions, and concludes by addressing the applications of docking in virtual screening, alongside current challenges within existing docking methods.</p>","PeriodicalId":45018,"journal":{"name":"Communications in Information and Systems","volume":"24 3","pages":"199-230"},"PeriodicalIF":0.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11583305/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142711419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-01-01Epub Date: 2024-10-21DOI: 10.4310/cis.241021213225
Jun Li, Nils G Walter, Shi-Jie Chen
Single-molecule Förster Resonance Energy Transfer (smFRET) is a powerful biophysical technique that utilizes the distance-dependent energy transfer between donor and acceptor dyes linked to individual molecules, providing insights into molecular conformational changes and interactions at the single-molecule level. Prior investigations leveraged smFRET to study the conformational dynamics of single truncated Ubc4 pre-mRNA molecules during splicing, yet these efforts did not prioritize structural modeling. In this study, we develop an smFRET-assisted RNA prediction method to predict the 2D and 3D structures of this pre-mRNA. To achieve this, we initiate the process by generating RNA structural ensembles through coarse-grained molecular dynamics (MD) simulations. Subsequently, inter-dye distances are calculated for these RNA structural ensembles by performing all-atom MD simulations of the dye groups. The ultimate determination of the 2D and 3D structures for the pre-mRNA is achieved by comparing the calculated inter-dye distances with experimental counterparts. Notably, our computational results demonstrate a significant alignment with experimental findings, which involve a conformational change at the 2D level.
{"title":"smFRET-assisted RNA structure prediction.","authors":"Jun Li, Nils G Walter, Shi-Jie Chen","doi":"10.4310/cis.241021213225","DOIUrl":"https://doi.org/10.4310/cis.241021213225","url":null,"abstract":"<p><p>Single-molecule Förster Resonance Energy Transfer (smFRET) is a powerful biophysical technique that utilizes the distance-dependent energy transfer between donor and acceptor dyes linked to individual molecules, providing insights into molecular conformational changes and interactions at the single-molecule level. Prior investigations leveraged smFRET to study the conformational dynamics of single truncated Ubc4 pre-mRNA molecules during splicing, yet these efforts did not prioritize structural modeling. In this study, we develop an smFRET-assisted RNA prediction method to predict the 2D and 3D structures of this pre-mRNA. To achieve this, we initiate the process by generating RNA structural ensembles through coarse-grained molecular dynamics (MD) simulations. Subsequently, inter-dye distances are calculated for these RNA structural ensembles by performing all-atom MD simulations of the dye groups. The ultimate determination of the 2D and 3D structures for the pre-mRNA is achieved by comparing the calculated inter-dye distances with experimental counterparts. Notably, our computational results demonstrate a significant alignment with experimental findings, which involve a conformational change at the 2D level.</p>","PeriodicalId":45018,"journal":{"name":"Communications in Information and Systems","volume":"24 3","pages":"163-179"},"PeriodicalIF":0.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11545564/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142636149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-01-01DOI: 10.4310/cis.2023.v23.n3.a4
King-Yeung Lam, Yuan Lou, Shizhao Ma
{"title":"Exploring the evolutionary dynamics of infectious diseases through SIS epidemic models","authors":"King-Yeung Lam, Yuan Lou, Shizhao Ma","doi":"10.4310/cis.2023.v23.n3.a4","DOIUrl":"https://doi.org/10.4310/cis.2023.v23.n3.a4","url":null,"abstract":"","PeriodicalId":45018,"journal":{"name":"Communications in Information and Systems","volume":"135 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136302408","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}
Pub Date : 2023-01-01DOI: 10.4310/cis.2023.v23.n3.a1
Jong-Shenq Guo, Bei Hu, Robert Jensen, Stephen S.-T. Yau
{"title":"Preface of special issue dedicated to Professor Avner Friedman’s 90th birthday","authors":"Jong-Shenq Guo, Bei Hu, Robert Jensen, Stephen S.-T. Yau","doi":"10.4310/cis.2023.v23.n3.a1","DOIUrl":"https://doi.org/10.4310/cis.2023.v23.n3.a1","url":null,"abstract":"","PeriodicalId":45018,"journal":{"name":"Communications in Information and Systems","volume":"83 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136302435","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}
Pub Date : 2023-01-01DOI: 10.4310/cis.2023.v23.n2.a1
Nan Zhao, Xinqi Gong
{"title":"A review of computational models for predicting protein-protein interaction and non-interaction","authors":"Nan Zhao, Xinqi Gong","doi":"10.4310/cis.2023.v23.n2.a1","DOIUrl":"https://doi.org/10.4310/cis.2023.v23.n2.a1","url":null,"abstract":"","PeriodicalId":45018,"journal":{"name":"Communications in Information and Systems","volume":"1 1","pages":"15-184"},"PeriodicalIF":0.9,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70404387","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}
Pub Date : 2023-01-01DOI: 10.4310/cis.2023.v23.n3.a2
Jong-Shenq Guo, Karen Guo, Paul Schrater
{"title":"Prediction of human looking behavior using interest-based image representations","authors":"Jong-Shenq Guo, Karen Guo, Paul Schrater","doi":"10.4310/cis.2023.v23.n3.a2","DOIUrl":"https://doi.org/10.4310/cis.2023.v23.n3.a2","url":null,"abstract":"","PeriodicalId":45018,"journal":{"name":"Communications in Information and Systems","volume":"21 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136302095","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}
Pub Date : 2023-01-01DOI: 10.4310/cis.2023.v23.n3.a3
Yaodan Huang, Bei Hu
{"title":"Periodic solution for a free boundary problem modeling small plaques","authors":"Yaodan Huang, Bei Hu","doi":"10.4310/cis.2023.v23.n3.a3","DOIUrl":"https://doi.org/10.4310/cis.2023.v23.n3.a3","url":null,"abstract":"","PeriodicalId":45018,"journal":{"name":"Communications in Information and Systems","volume":"72 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136302393","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}
Pub Date : 2023-01-01DOI: 10.4310/cis.2023.v23.n3.a5
Allen Montz, Hamid Bellout, Frederick Bloom
{"title":"Flow of an incompressible nonlinear bipolar viscous fluid in a sinusoidally constricted channel","authors":"Allen Montz, Hamid Bellout, Frederick Bloom","doi":"10.4310/cis.2023.v23.n3.a5","DOIUrl":"https://doi.org/10.4310/cis.2023.v23.n3.a5","url":null,"abstract":"","PeriodicalId":45018,"journal":{"name":"Communications in Information and Systems","volume":"98 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136302444","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}
Pub Date : 2023-01-01DOI: 10.4310/cis.2023.v23.n2.a3
Xu-Qiang Hu, Zi-Xin Zou, Dinesh Manocha
We present a novel solution, TSDFFilter, for remote 3D reconstruction to relieve the high bandwidth requirement problem. Our approach is designed for scenarios where agents are used to collect data using an RGB-D camera and then transmit the information over the regular network to a high-performance server, where a global, dense, and volumetric model of a real-world scene is reconstructed. Our approach uses a content-aware communication planning framework in which agents can prune the gathered RGB-D information according to the transmission policy generated by the server. To generate the transmission policy, we introduce a confidence value to estimate how much each RGB-D pixel contributes to the reconstruction quality, and present an algorithm to find the confidence value. As a result, agents can transmit less RGB-D information without blindly compromising the reconstruction quality as the key-frame method and down-sampling method do. We implement our TSDFFilter framework to achieve real-time agent-assisted 3D reconstruction. Extensive evaluations show that comparing with the key-frame and down-sampling methods, our TSDFFil-ter framework can reduce the bandwidth requirement by up to 36% with similar reconstruction Chamfer distance, and reduce the reconstruction Chamfer distance by up to 78% with similar bandwidth requirement.
{"title":"TSDFFilter: content-aware communication planning for remote 3D reconstruction","authors":"Xu-Qiang Hu, Zi-Xin Zou, Dinesh Manocha","doi":"10.4310/cis.2023.v23.n2.a3","DOIUrl":"https://doi.org/10.4310/cis.2023.v23.n2.a3","url":null,"abstract":"We present a novel solution, TSDFFilter, for remote 3D reconstruction to relieve the high bandwidth requirement problem. Our approach is designed for scenarios where agents are used to collect data using an RGB-D camera and then transmit the information over the regular network to a high-performance server, where a global, dense, and volumetric model of a real-world scene is reconstructed. Our approach uses a content-aware communication planning framework in which agents can prune the gathered RGB-D information according to the transmission policy generated by the server. To generate the transmission policy, we introduce a confidence value to estimate how much each RGB-D pixel contributes to the reconstruction quality, and present an algorithm to find the confidence value. As a result, agents can transmit less RGB-D information without blindly compromising the reconstruction quality as the key-frame method and down-sampling method do. We implement our TSDFFilter framework to achieve real-time agent-assisted 3D reconstruction. Extensive evaluations show that comparing with the key-frame and down-sampling methods, our TSDFFil-ter framework can reduce the bandwidth requirement by up to 36% with similar reconstruction Chamfer distance, and reduce the reconstruction Chamfer distance by up to 78% with similar bandwidth requirement.","PeriodicalId":45018,"journal":{"name":"Communications in Information and Systems","volume":"1 1","pages":"213-239"},"PeriodicalIF":0.9,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70404404","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}
Pub Date : 2023-01-01DOI: 10.4310/cis.2023.v23.n2.a2
Hongmei Yang, Yanqi Liu, Xiaoqiu Jiang, Xinqi Gong
{"title":"Quantitative anatomy of characteristics and influencing factors of PM2.5 and O3 in Liaoning province of China","authors":"Hongmei Yang, Yanqi Liu, Xiaoqiu Jiang, Xinqi Gong","doi":"10.4310/cis.2023.v23.n2.a2","DOIUrl":"https://doi.org/10.4310/cis.2023.v23.n2.a2","url":null,"abstract":"","PeriodicalId":45018,"journal":{"name":"Communications in Information and Systems","volume":"1 1","pages":"185-212"},"PeriodicalIF":0.9,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70404396","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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