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A Searchable Database of Crystallization Cocktails in the PDB: Analyzing the Chemical Condition Space

Miranda L. Lynch, Max F. Dudek, Sarah E.J. Bowman
2020 Patterns  
Here, we present a searchable database of the chemicals associated with successful crystallization experiments from the PDB.  ...  A major bottleneck in determining MX structures is finding conditions in which a biomolecule will crystallize.  ...  DECLARATION OF INTERESTS The authors declare no competing interests.  ... 
doi:10.1016/j.patter.2020.100024 pmid:32776019 pmcid:PMC7409820 fatcat:npezmrpktvaepa273zq3kwuj4u

In Silico Identification and In Vitro and In Vivo Validation of Anti-Psychotic Drug Fluspirilene as a Potential CDK2 Inhibitor and a Candidate Anti-Cancer Drug

Xi-Nan Shi, Hongjian Li, Hong Yao, Xu Liu, Ling Li, Kwong-Sak Leung, Hsiang-fu Kung, Di Lu, Man-Hon Wong, Marie Chia-mi Lin, Yu-Jia Chang
2015 PLoS ONE  
In view of the fact that fluspirilene has a long history of PLOS ONE |  ...  In particular, CDK2 is a key factor regulating the cell cycle G1 to S transition and a hallmark for cancers.  ...  The cells were then analyzed using flow cytometry (CyFlow Space/Partec, Germany).  ... 
doi:10.1371/journal.pone.0132072 pmid:26147897 pmcid:PMC4493148 fatcat:dpwnrmgatvblvcf6wwvlp3afpu

BioExcel-2 Deliverable D3.3 – Use Case Progress Report

Arno Proeme, Alessandra Villa, Zuzana Jandova, Alexandre Bonvin, Vytautas Gapsys, Adam Hospital, Yvonne Westermaier, Gerrit Groenhof, Dmitry Morozon, Vaibhav Modi, Emiliano Ippolilit
2020 Zenodo  
This report describes progress made during the first 18 months of BioExcel-2 executing the project's planned demonstrator research projects (the "Use Cases") as well as research work done by BioExcel in  ...  In Use Case 2, parallel execution of containerised HADDOCK and the necessary data movement underpinning this execution is similarly orchestrated by PyCO [...]  ...  In one case (PDB ID 3V6Z), a slightly better performance of HADDOCK docking is observed when two simulated apo structures m(Abs-Ags) are used instead of two crystal apo structures (m(Ab-Ag) hq).  ... 
doi:10.5281/zenodo.5511684 fatcat:civldhbeljctpkcdtay7dvkds4

A Sec14-like phosphatidylinositol transfer protein paralog defines a novel class of heme-binding proteins

Danish Khan, Dongju Lee, Gulcin Gulten, Anup Aggarwal, Joshua Wofford, Inna Krieger, Ashutosh Tripathi, John W Patrick, Debra M Eckert, Arthur Laganowsky, James Sacchettini, Paul Lindahl (+1 others)
2020 eLife  
The collective data identify Sfh5 as the prototype of a new class of fungal hemoproteins, and emphasize the versatility of the Sec14-fold as scaffold for translating the binding of chemically distinct  ...  ligands to the control of diverse sets of cellular activities.  ...  These data are adapted from the following 1232 searchable database (  ... 
doi:10.7554/elife.57081 pmid:32780017 pmcid:PMC7462610 fatcat:vbh3aanqsrg5lo7gd6kfhwk3au

Verbesserter Ansatz zum Ligand growing durch Fragment docking und dem designen von Fragment Bibliotheken

Florent Chevillard, Kolb, Peter (Dr.)
In the past two decades, fragment-based drug discovery (FBDD) has continuously gained popularity in drug discovery efforts and has become a dominant tool in order to explore novel chemical entities that  ...  In a first study focusing on the $beta_{2}$AR, we suggested a total of eight diverse extensions for different fragment hits using PINGUI.  ...  Acknowledgements 192 Acknowledgements Research in the science field is a treacherous path, made of twists, turns and dead-ends.  ... 
doi:10.17192/z2016.0809 fatcat:m6thmsigpballeexpw26ztummq

Top-down and middle-down mass spectrometry structural characterization of monoclonal antibodies

Luca Fornelli
Acknowledgements The authors are grateful to Aleksey Vorobyev and Hisham Ben Hamidane for the assistance in the experimental work.  ...  A.W.S. is grateful to Biomedizin-Naturwissenschaft-Forschung (BNF, University of Bern, Switzerland) for the personal financial support.  ...  database, or, in the case of middle-down and bottomup approaches, in a database composed of peptides obtained by in silico digestion of the same proteins).  ... 
doi:10.5075/epfl-thesis-6052 fatcat:zvzne2iulradpdwrq7rtmmsn3u

Structural and functional characterisation of peptide inhibitors of voltage-gated sodium channels from piscivorous cone snails

Brad Reed Green
One member of the µ-conotoxin family, µ-BuIIIB, is of interest for its purported role in inhibiting the sodium channel subtype NaV1.3. Chapter 4 describes efforts to [...]  ...  The venoms of piscivorous (fish-hunting) snails of the genus Conus contain a vast array of neuroactive peptides used to immobilize prey and for defence.  ...  This work was supported by National Institutes of ACKNOWLEDGMENTS. We thank the following for providing rat clones: Prof. Alan A. Goldin (University of California), Na V 1.1 to -1.5, Na V 1.  ... 
doi:10.4225/03/58b7821b905ef fatcat:rhvk4vs4yjhk3kbukklay5rdmm

The Sentinel Initiative as a Knowledge Commons [chapter]

Ryan Abbott, Katherine J. Strandburg, Brett M. Frischmann, Michael J. Madison
Governing Medical Knowledge Commons  
The editors' previous volume, Governing Knowledge Commons, demonstrated the framework's power through case studies in a diverse range of areas.  ...  a practical introduction to the knowledge commons framework and a synthesis of conclusions and lessons.  ...  Interestingly, in a system built on openness and designed to avoid intellectual property claims, this centralized structure establishes something of a proprietary interest in the data on the part of the  ... 
doi:10.1017/9781316544587.007 fatcat:lefya2gjp5hwnfdvl4fnjqdrvq