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High end GPCR design: crafted ligand design and druggability analysis using protein structure, lipophilic hotspots and explicit water networks

Jonathan S Mason, Andrea Bortolato, Dahlia R Weiss, Francesca Deflorian, Benjamin Tehan, Fiona H Marshall
2013 In Silico Pharmacology  
Conclusions: The promise of full structure-based drug design (SBDD) for GPCRs is now possible using a combination of advanced experimental and computational data.  ...  Results: Analysis of diverse ligands binding to the adenosine A 2A receptor together with new structures for the δ/κ/μ opioid and CCR5 receptors confirmed the key role of lipophilic hotspots in driving  ...  Acknowledgements The authors wish to thank Gabriele Cruciani, Massimo Baroni and Simon Cross for valued scientific discussions and the development of the WaterFLAP software and Steve Andrews and Miles  ... 
doi:10.1186/2193-9616-1-23 fatcat:jxt47ssec5bavgizayytobivge

PyLipID: A Python package for analysis of protein-lipid interactions from MD simulations [article]

Wanling Song, Robin A. Corey, Bertie Ansell, Keith Cassidy, Michael Horrell, Anna Duncan, Phillip James Stansfeld, Mark Sansom
2021 biorxiv/medrxiv   pre-print
We introduce PyLipID, a python package for the identification and characterization of specific lipid interactions and binding sites on membrane proteins from molecular dynamics simulations.  ...  PyLipID uses a community analysis approach for binding site detection, calculating lipid residence times for both the individual protein residues and the detected binding sites.  ...  For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.  ... 
doi:10.1101/2021.07.14.452312 fatcat:l767bfzar5f4blmxrflnb4tfka

Open source molecular modeling

Somayeh Pirhadi, Jocelyn Sunseri, David Ryan Koes
2016 Journal of Molecular Graphics and Modelling  
Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable.  ...  In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry.  ...  helpful feedback on a draft of this manuscript.  ... 
doi:10.1016/j.jmgm.2016.07.008 pmid:27631126 pmcid:PMC5037051 fatcat:jxdvghsiszadjevub22qbjywwm

Intermolecular Interactions in Functional Crystalline Materials: From Data to Knowledge

Anna V. Vologzhanina
2019 Crystals  
Intermolecular interactions of organic, inorganic, and organometallic compounds are the key to many composition–structure and structure–property networks.  ...  Besides, some unusual applications, the potential for further development and limitations of the CCDC software are reported.  ...  Acknowledgments: The author is grateful to A. A. Korlyukov for fruitful discussion of the text. Conflicts of Interest: The author declares no conflict of interest. Crystals 2019, 9, 478  ... 
doi:10.3390/cryst9090478 fatcat:ums262nlvnd4rigjvhbjtrxxxm

How do Molecular Dynamics Data Complement Static Structural Data of GPCRs

Mariona Torrens-Fontanals, Tomasz Maciej Stepniewski, David Aranda-García, Adrián Morales-Pastor, Brian Medel-Lacruz, Jana Selent
2020 International Journal of Molecular Sciences  
Here, we review the contribution of MD simulations to complement static structural data and to improve our understanding of GPCR physiology and pharmacology, as well as the challenges that still need to  ...  Due to this dynamic nature, a static snapshot does not fully explain the complexity of GPCR signal transduction.  ...  One of the most widely used structure-based drug design strategies is virtual screening, where libraries of small molecules are screened to identify those structures which most likely bind to the target  ... 
doi:10.3390/ijms21165933 pmid:32824756 pmcid:PMC7460635 fatcat:pt5q646tevbghcv2ne4hbwdjlu

Innovative in Silico Approaches for Characterization of Genes and Proteins

Gh. Rasool Bhat, Itty Sethi, Bilal Rah, Rakesh Kumar, Dil Afroze
2022 Frontiers in Genetics  
It is a science which gathers the information from biology in terms of molecules and applies the informatic techniques to the gathered information for understanding and organizing the data in a useful  ...  Additionally, rapid advancement in proteomics have steered researchers to organize the study of protein structure, function, relationships, and dynamics in space and time.  ...  NGS has opened a new way to analyze/detect the RNA molecules present in the biological samples.  ... 
doi:10.3389/fgene.2022.865182 pmid:35664302 pmcid:PMC9159363 fatcat:mbz7ci3s25eudn7qmqch5xghci

The 18th European Symposium on Quantitative Structure–Activity Relationships

Anna Tsantili-Kakoulidou, Dimitris K Agrafiotis
2011 Expert Opinion on Drug Discovery  
Finally we want to thank to Prof. Wigley for the contribution to this work with the x-ray structure of the protein ligand to the GR1222222.  ...  Furthermore, the conducted docking studies elucidated the possible alternative binding mode of the ligands into the ATP binding cleft and assigned their physicochemical and structural features which promote  ...  flexibility for structure-based design of ligands binding to acetycholinesterase.  ... 
doi:10.1517/17460441.2011.560604 pmid:22646021 fatcat:tb4bhvtnpzahxm4xba7iw4afuy

Discovery of Human Signaling Systems: Pairing Peptides to G Protein-Coupled Receptors

Simon R. Foster, Alexander S. Hauser, Line Vedel, Ryan T. Strachan, Xi-Ping Huang, Ariana C. Gavin, Sushrut D. Shah, Ajay P. Nayak, Linda M. Haugaard-Kedström, Raymond B. Penn, Bryan L. Roth, Hans Bräuner-Osborne (+1 others)
2019 Cell  
This integrated computational and multifaceted experimental approach expands the peptide-GPCR network and opens the way for studies to elucidate the roles of these signaling systems in human physiology  ...  Integrating comparative genomics across 313 species and bioinformatics on all protein sequences and structures of human class A GPCRs, we identify universal characteristics that uncover additional potential  ...  more complex than small molecules, due to greater size and conformational freedom.  ... 
doi:10.1016/j.cell.2019.10.010 pmid:31675498 pmcid:PMC6838683 fatcat:usfzdv75rvc55pqiyh65ikq44a

Biotin proximity tagging favours unfolded proteins and enables the study of intrinsically disordered regions

David-Paul Minde, Manasa Ramakrishna, Kathryn S. Lilley
2020 Communications Biology  
We conclude that biotin proximity tagging favours sites of local disorder in proteins and suggest the possibility of using biotin painting as a method to gain unique insights into in vivo condition-dependent  ...  We show that in a biotin 'painting' time course experiment, biotinylation events in Escherichia coli ribosomes progress from unfolded and exposed regions at 10 s, to structured and less accessible regions  ...  We thank Dewi Eburne for help with exploratory experiments that triggered our interest in structural features of biotinomes, Prof. Ben Luisi for the kind gift of highly purified 70S ribosomes, Dr.  ... 
doi:10.1038/s42003-020-0758-y pmid:31969649 fatcat:lpx2m6tgffhlrkwtako5encz24

Cellular labelling favours unfolded proteins [article]

David-Paul Minde, Manasa Ramakrishna, Kathryn Susan Lilley
2018 bioRxiv   pre-print
The extent of foldability of predicted IDRs is difficult to measure due to significant technical challenges to survey in vivo protein conformations on a proteome-wide scale.  ...  We show that biotin painting is a promising approach to fill gaps in knowledge between static in vitro protein structures, in silico disorder predictions and in vivo condition-dependent subcellular plasticity  ...  D.P.M. is supported by the BBSRC grant BB/N010493/1 and a TMT grant (Thermo Fisher, 2018) for studying cellular biotinylations.  ... 
doi:10.1101/274761 fatcat:yzrpf3tejbcw5afnyzhrknqdo4

WILDS: A Benchmark of in-the-Wild Distribution Shifts [article]

Pang Wei Koh, Shiori Sagawa, Henrik Marklund, Sang Michael Xie, Marvin Zhang, Akshay Balsubramani, Weihua Hu, Michihiro Yasunaga, Richard Lanas Phillips, Irena Gao, Tony Lee, Etienne David (+11 others)
2021 arXiv   pre-print
To address this gap, we present WILDS, a curated benchmark of 10 datasets reflecting a diverse range of distribution shifts that naturally arise in real-world applications, such as shifts across hospitals  ...  This gap remains even with models trained by existing methods for tackling distribution shifts, underscoring the need for new methods for training models that are more robust to the types of distribution  ...  We are grateful for all of the helpful suggestions and constructive feedback from: Aditya Khosla, Andreas Schlueter, Annie Chen, Aleksander Madry, Alexander D'Amour, Allison Koenecke We also gratefully  ... 
arXiv:2012.07421v3 fatcat:bsohmukpszajxeadeo25oxmbs4

Abstracts from the 26th European Society for Animal Cell Technology Meeting - Cell culture technologies: bridging academia and industry to provide solutions for patients

2020 BMC Proceedings  
Enhanced process understanding and multivariate prediction of the relationship between cell culture process and monoclonal antibody quality.  ...  Acknowledgements We appreciate the support provided by Pall's bioreactor applications scientists and a special thank you to Todd Lundeen for his considerable dedication.  ...  In step 2, a DoE with small-scale semi-continuous perfusion models was applied to optimize the pre-selected feed supplements and to establish valid regression models (B.).  ... 
doi:10.1186/s12919-020-00188-y fatcat:6kscifx565appmxq57svl42biy

A 3D grid based tool kit for protein crystal structure ensemble analysis

Sophie Weber
2018 unpublished
The visualisation and qualitative analysis provides an overview of structural differences and should help to drive decisions for drug design. Grid maps are the main topic of this thesis.  ...  Since a plethora of protein-ligand complex structures are available in pharmaceutical industry, the analysis of protein crystal structure ensembles has become a new task in the field of drug design.  ...  SBDD Structure Based Drug Design.  ... 
doi:10.25365/thesis.52455 fatcat:acbqg33m7zd7he23iqnj23w4ia

Comparative Analysis of Different Machine Learning Classifiers for the Prediction of Chronic Diseases [chapter]

Rajesh Singh, Anita Gehlot, Dharam Buddhi
2022 Comparative Analysis of Different Machine Learning Classifiers for the Prediction of Chronic Diseases  
This paper forms the basis of understanding the difficulty of the domain and the amount of efficiency achieved by the various methods recently.  ...  Precise diagnosis of these diseases on time is very significant for maintaining a healthy life.  ...  However, still further research is needed to overcome the challenges and making the Stirling engine commercially viable and cost effective. for multiple applications.  ... 
doi:10.13052/rp-9788770227667 fatcat:da47mjbbyzfwnbpde7rgbrlppe

Abstracts from the 2018 OAS Annual Meeting

The Ohio Academy of Science
2018 The Ohio journal of science  
Abstracts from the 2018 Ohio Academy of Science Annual Meeting  ...  The arrival of modern designer drugs brings the need for more accurate and reliable testing methods for these new drugs. These methods must be rapid and useful for more than just one specific drug.  ...  The packaging plasmid expresses a fusion protein consisting of curli fibers and cellulose binding do-mains.  ... 
doi:10.18061/ojs.v118i1.6338 fatcat:24esdpldjvhppbs7q5smhx6sbq
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