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ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement

K. Suhre, Y.-H. Sanejouand
2004 Nucleic Acids Research  
Normal mode analysis (NMA) is a powerful tool for predicting the possible movements of a given macromolecule.  ...  Here we present ElNémo, a web interface to the Elastic Network Model that provides a fast and simple tool to compute, visualize and analyse lowfrequency normal modes of large macro-molecules and to generate  ...  ACKNOWLEDGEMENTS Molscript (27) and LSQMAN from the Déj a aVu package (25) are used by the server. VMD (28) was used to generate some of the examples.  ... 
doi:10.1093/nar/gkh368 pmid:15215461 pmcid:PMC441506 fatcat:3k5xwemuazhrjpqyojw3bhfxca

elNémo: using normal mode analysis in molecular replacement

K. Suhre, Y.-H. Sanejouand
2005 Acta Crystallographica Section A Foundations of Crystallography  
We outline possible protocols of using NMA in MR and present the web-server elNémo [2] for online NMA template generation http://igs-server.cnrs-mrs.fr/elnemo/index.html.  ...  Normal mode analysis (NMA) is a powerful tool for predicting the possible movements of a given macromolecule.  ... 
doi:10.1107/s0108767305095164 fatcat:2c545k5g7nddzcvs4wbubelwy4

Present status of electron crystallography on inorganic materials

T. E. Weirich
2005 Acta Crystallographica Section A Foundations of Crystallography  
We outline possible protocols of using NMA in MR and present the web-server elNémo [2] for online NMA template generation http://igs-server.cnrs-mrs.fr/elnemo/index.html.  ...  Normal mode analysis (NMA) is a powerful tool for predicting the possible movements of a given macromolecule.  ... 
doi:10.1107/s0108767305095152 fatcat:ikblbqccmffctji4f3sm7rqdca

Structural and charge-density studies of transition-metal oxides using convergent-beam electron diffraction

K. Tsuda
2005 Acta Crystallographica Section A Foundations of Crystallography  
We outline possible protocols of using NMA in MR and present the web-server elNémo [2] for online NMA template generation http://igs-server.cnrs-mrs.fr/elnemo/index.html.  ...  Normal mode analysis (NMA) is a powerful tool for predicting the possible movements of a given macromolecule.  ... 
doi:10.1107/s0108767305095140 fatcat:dr3p2b6ujbe4va3z2tekqj6vb4

Refinement when amplitudes aren't enough: real-space, H-bonding and electrostatics

M. S. Chapman, F. Fabiola, A. Korostelev, M. Fenley
2005 Acta Crystallographica Section A Foundations of Crystallography  
Databases: Database searching using the Cambridge Structural Database (CSD) [3] can produce thousands of 'hits' if a simple fragment is used, and as a result processing and interpreting the results becomes  ...  Pattern matching in powder X-ray diffraction: High throughput screening experiments designed to search for polymorphs and salts of drug candidates use PXRD to characterize the results, and this produces  ...  We outline possible protocols of using NMA in MR and present the web-server elNémo [2] for online NMA template generation http://igs-server.cnrs-mrs.fr/elnemo/index.html.  ... 
doi:10.1107/s0108767305095176 fatcat:mcqji5b5evcidfnkse6kph3lhm

Incomensurate modulated structure determination by combining HREM and ED

F. Li, H. Fan
2005 Acta Crystallographica Section A Foundations of Crystallography  
Normal mode analysis (NMA) is a powerful tool for predicting the possible movements of a given macromolecule.  ...  We outline possible protocols of using NMA in MR and present the web-server elNémo [2] for online NMA template generation http://igs-server.cnrs-mrs.fr/elnemo/index.html. [1] Suhre K., Sanejouand Y.H.,  ...  On the other end of the spectrum computer simulations of molecular dynamics may be able to predict structures of small proteins based on force fields within the near future.  ... 
doi:10.1107/s0108767305095139 fatcat:gsnyquybvvf6zmctaxwjeeelhy

STRUCTURAL INSIGHTS INTO THE ENZYME MECHANISM OF A NEW FAMILY OF D-2-HYDROXYACID DEHYDROGENASES, A CLOSE HOMOLOG OF 2-KETOPANTOATE REDUCTASE

SUKANTA MONDAL, KENJI MIZUGUCHI
2009 Genome Informatics 2009  
To explore large conformational transitions (domain motions), a normal mode analysis was employed using a simple potential and the protein models.  ...  Our findings will be useful for site-directed mutagenesis studies and protein engineering.  ...  Acknowledgments This work was in part supported by the Knowledge Cluster Initiative (stage II) by the MEXT (Ministry of Education, Culture, Sports, Science and Technology). We thank Dr. Lokesh P.  ... 
doi:10.1142/9781848165632_0009 fatcat:c7w3nqi3argxnj7zgj4kse74xa

Dealing with structural variability in molecular replacement and crystallographic refinement through normal-mode analysis

Marc Delarue
2007 Acta Crystallographica Section D: Biological Crystallography  
Other simpler approaches consist of generating systematically perturbed models along one particular mode using, for example, the elNémo web server and then proceeding with the standard MR procedure into  ...  Conclusion Because the normal-mode representation of conformational flexibility has been validated both through the analysis of a database of protein movements and correlation with experimental B factors  ... 
doi:10.1107/s0907444907053516 pmid:18094466 pmcid:PMC2394787 fatcat:wx32za7725fgznxa346pp6g2qi

MOLECULAR DYNAMICS AND CONFORMATIONAL FLEXIBILITY IN HEAT SHOCK PROTEIN 60.2 OF MYCOBACTERIUM TUBERCULOSIS

Gollapalli Pavan, Manjunatha Hanumanthappa
2015 International Journal for Computational Biology  
Normal mode analysis was also performed to study the conformation and direction of motion of a protein under study for a large time scale simulation.  ...  Hence it is provided and drawn a clear path between role of chaperon in protein folding and their role in the infection showing the immunological importance of Heat Shock Protein 60.2.  ...  ACKNOWLEDGEMENTS We gratefully acknowledge for the award of INSPIRE fellowship from the Department of Science and Technology (DST), New Delhi, India for the financial support and encouragement.  ... 
doi:10.34040/ijcb.4.2.2015.59 fatcat:m4ne6ld4lfh45be2tr76lzwcoe

SCEDS: protein fragments for molecular replacement inPhaser

Airlie J. McCoy, Robert A. Nicholls, Thomas R. Schneider
2013 Acta Crystallographica Section D: Biological Crystallography  
A method is described for generating protein fragments suitable for use as molecular-replacement (MR) template models.  ...  The template model for a protein suspected to undergo a conformational change is perturbed along combinations of low-frequency normal modes of the elastic network model.  ...  A method is described for generating protein fragments suitable for use as molecular-replacement (MR) template models.  ... 
doi:10.1107/s0907444913021811 pmid:24189233 pmcid:PMC3817695 fatcat:3ydgajinrnbdpejlzq24rkxsoq

Molecular modelling and simulations in cancer research

Ran Friedman, Kjetil Boye, Kjersti Flatmark
2013 Biochimica et Biophysica Acta. CR. Reviews on Cancer  
dynamics 14 NMA -normal mode analysis 15 QM -quantum mechanics 16 QM/MM -quantum mechanics / molecular mechanics 17 SAXS -small angle X-ray scattering 18 YAS -yttrium-alumino-silicate 19 20 A large number  ...  In the field of computer-aided drug design, MD simulations can 131 infer on correct and incorrect modes of binding of a molecule [13] and the energetics of the binding reac-132 tion, e.g., the interplay  ...  The calculations are both simpler and faster than atomistic normal mode analysis 393 (section 2.1.6), and can therefore be routinely carried out by use of dedicated web servers (Table A .5), 394 without  ... 
doi:10.1016/j.bbcan.2013.02.001 pmid:23416097 fatcat:6wyfplnxdzdpdhhbf25ln7itry

iGNM: a database of protein functional motions based on Gaussian Network Model

L.-W. Yang, X. Liu, C. J. Jursa, M. Holliman, A.J. Rader, H. A. Karimi, I. Bahar
2005 Bioinformatics  
Static and animated images for describing the conformational mobility of proteins over a broad range of normal modes are accessible, along with an online calculation engine available for newly deposited  ...  Results: We computed the GNM dynamics for 20 058 structures from the Protein Data Bank, and generated information on the equilibrium dynamics at the level of individual residues.  ...  Partial support by the NSF-ITR grant #EIA-0225636 and the NIH grant #1 R01 LM007994-01A1 is gratefully acknowledged.  ... 
doi:10.1093/bioinformatics/bti469 pmid:15860562 pmcid:PMC1752228 fatcat:vrtcjabj5rbclkv376yudvnybq

Recent developments in phasing and structure refinement for macromolecular crystallography

Paul D Adams, Pavel V Afonine, Ralf W Grosse-Kunstleve, Randy J Read, Jane S Richardson, David C Richardson, Thomas C Terwilliger
2009 Current Opinion in Structural Biology  
Central to crystallographic structure solution is obtaining accurate phases in order to build a molecular model, ultimately followed by refinement of that model to optimize its fit to the experimental  ...  Recent advances in phasing and model refinement and validation algorithms make it possible to arrive at better electron density maps and more accurate models.  ...  Acknowledgements The authors would like to thank the NIH for their support (1P01 GM063210). This work was partially supported by the US Department of Energy under Contract No. DE-AC02-05CH11231.  ... 
doi:10.1016/j.sbi.2009.07.014 pmid:19700309 pmcid:PMC2763973 fatcat:ewxfxsuqcnbmrhvsgsi5g6ybjm

Breakage of the Oligomeric CaMKII Hub by the Regulatory Segment of the Kinase

Deepti Karandur, Moitrayee Bhattacharyya, Zijie Xia, Young Kwang Lee, Serena Muratcioglu, Darren McAffee, Ethan McSpadden, Baiyu Qiu, Jay T Groves, Evan R Williams, John Kuriyan
2020 eLife  
Single-molecule fluorescence intensity analysis of CaMKII-α expressed in mammalian cells shows that activation of CaMKII-α results in the destabilization of the holoenzyme.  ...  Ca2+/calmodulin dependent protein kinase II (CaMKII) is an oligomeric enzyme with crucial roles in neuronal signaling and cardiac function.  ...  ElNemo: a normal mode web server for protein 885 movement analysis and the generation of templates for molecular replacement. Nucleic Acids 886 Research 32(Web Server issue), pp.  ... 
doi:10.7554/elife.57784 pmid:32902386 pmcid:PMC7538161 fatcat:y3omshpzrfavnomcdltjxzdl2e

Buried and Accessible Surface Area Control Intrinsic Protein Flexibility

Joseph A. Marsh
2013 Journal of Molecular Biology  
Overall this work provides both fundamental mechanistic insight into the origin of protein flexibility and a simple, practical method for predicting flexibility from protein structures.  ...  There is also a strong tendency for the crystal structures of more flexible proteins to be solved to lower resolutions.  ...  ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Research 32, W610-W614 39.  ... 
doi:10.1016/j.jmb.2013.06.019 pmid:23811058 fatcat:lbmicbpzb5ho7pbnkvf7zjkv6e
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