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Visual exploration of large normal mode spaces to study protein flexibility

Pierre Bedoucha, Nathalie Reuter, Helwig Hauser, Jan Byška
2020 Computers & graphics  
Finally, to further steer the exploration of the large normal mode space, we utilized the sorting approach of the modes in the SNMV.  ...  A commonly used alternative to MD simulations, which is better suited for studying large molecular systems for longer time intervals, is to decompose the flexibility of a protein into a set of normal modes  ... 
doi:10.1016/j.cag.2020.05.025 fatcat:nu6zyas5jbarrlm572vjkwcqaq

NMSim Web Server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins

D. M. Kruger, A. Ahmed, H. Gohlke
2012 Nucleic Acids Research  
Second, a rigid cluster normal-mode analysis provides lowfrequency normal modes.  ...  The approach allows performing three simulation types: unbiased exploration of conformational space; pathway generation by a targeted simulation; and radius of gyrationguided simulation.  ...  ACKNOWLEDGEMENTS We are grateful to Prof. Michael F. Thorpe (Arizona State University) for granting a FIRST license.  ... 
doi:10.1093/nar/gks478 pmid:22669906 pmcid:PMC3394247 fatcat:4mpljg6g2ndvfduymwdozlcegq

iMODS: internal coordinates normal mode analysis server

José Ramón López-Blanco, José I. Aliaga, Enrique S. Quintana-Ortí, Pablo Chacón
2014 Nucleic Acids Research  
Normal mode analysis (NMA) in internal (dihedral) coordinates naturally reproduces the collective functional motions of biological macromolecules. iMODS facilitates the exploration of such modes and generates  ...  The generated allheavy-atoms conformations can be used to introduce flexibility for more advanced modeling or sampling strategies.  ...  Gleicher for sharing the source code of their affine-model-based approach for the automated illustration of normal modes and Prof. S.  ... 
doi:10.1093/nar/gku339 pmid:24771341 pmcid:PMC4086069 fatcat:e3r4bfyt2jbsxdvhm4b2nkwbm4

Structure and Function in Homodimeric Enzymes: Simulations of Cooperative and Independent Functional Motions

Stephen A. Wells, Marc W. van der Kamp, John D. McGeagh, Adrian J. Mulholland, Claudio M Soares
2015 PLoS ONE  
motion, biased along normal mode directions, to identify relevant motions encoded in the protein structure.  ...  Geometric simulations correctly identify and explore large amplitudes of motion, while molecular dynamics simulations indicate the ranges of motion that are energetically feasible.  ...  The authors would like to thank Prof. Danson for helpful comments. Author Contributions  ... 
doi:10.1371/journal.pone.0133372 pmid:26241964 pmcid:PMC4524684 fatcat:6jwiyaya4fgmpdax5ycha3nzgu

Conformational Analysis of Clostridium difficile Toxin B and Its Implications for Substrate Recognition

Rebecca Swett, G. Andrés Cisneros, Andrew L. Feig, Jörg Langowski
2012 PLoS ONE  
To characterize the conformational space of TcdB, we applied normal mode and hinge-region analysis, followed by longtimescale unbiased molecular dynamics.  ...  TcdB is a large flexible protein that appears to undergo significant structural rearrangement upon accommodation of its substrates: UDP-glucose and a Rho-family GTPase.  ...  The combination of normal mode analysis, MD and GMD and PCA has been shown to be a very effective method for study of protein-protein interactions.  ... 
doi:10.1371/journal.pone.0041518 pmid:22844485 pmcid:PMC3402401 fatcat:dari2n2ddfbafk6mdszm3zsmhu

FlexServ: an integrated tool for the analysis of protein flexibility

J. Camps, O. Carrillo, A. Emperador, L. Orellana, A. Hospital, M. Rueda, D. Cicin-Sain, M. D'Abramo, J. L. Gelpi, M. Orozco
2009 Bioinformatics  
The server incorporates powerful protocols for the coarsegrained determination of protein dynamics using different versions of Normal Mode Analysis (NMA), Brownian dynamics (BD) and Discrete Dynamics (  ...  FlexServ is a web-based tool for the analysis of protein flexibility.  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btp304 pmid:19429600 fatcat:g7zc6ixjxveapfzkx2hqjckmy4

Hierarchical and multi-resolution representation of protein flexibility

Y. Zhao, D. Stoffler, M. Sanner
2006 Bioinformatics  
Moreover, the ability to assign shapes to the nodes in a FT allows the interactive manipulation of flexible protein shapes and the interactive visualization of the impact of conformational changes on the  ...  The FT structure makes it straightforward to combine and nest a wide variety of motion types such as hinge, shear, twist, screw, rotameric side chains, normal modes, essential dynamics, etc.  ...  ACKNOWLEDGEMENTS We thank Arthur Olson for fruitful discussions and the financial support from NIH Grant BISTI, GM65609, 2003-2007 to M Sanner and NIH RR08605, 2004-2009 to M Sanner.  ... 
doi:10.1093/bioinformatics/btl481 pmid:16984893 fatcat:jfsfommvaffnbfofhgf2srz7z4

A PCA-guided Search Algorithm to Probe the Conformational Space of the Ras Protein

Rudy Clausen, Amarda Shehu
2007 Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics - BCB'13  
We present a search algorithm to probe the conformational space of the RAS protein, a critical enzyme that employs conformational switching for its biological activity in the cell.  ...  A principal component analysis (PCA) over these structures provides directions for exploration, which are used in combination with energetic refinement to sample low-energy conformations of Ras.  ...  The PCA-guided approach here is similar to how Normal Mode Analysis has been used in other contexts and implementations to explore flexibility in peptides, protein loops, or protein binding sites [4]  ... 
doi:10.1145/2506583.2506681 dblp:conf/bcb/ClausenS13 fatcat:kf5bcuya2jhz7mhivztmo4qeu4

ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability

Vincent Frappier, Matthieu Chartier, Rafael J. Najmanovich
2015 Nucleic Acids Research  
The inclusion of this layer of information was shown to improve conformational space sampling and apply for the first time a coarse-grained normal mode analysis method to predict the effect of single point  ...  ENCoM is a coarse-grained normal mode analysis method recently introduced that unlike previous such methods is unique in that it accounts for the nature of amino acids.  ...  Among the main computational techniques to study protein dynamics are molecular dynamics (MD) and normal mode analysis (NMA).  ... 
doi:10.1093/nar/gkv343 pmid:25883149 pmcid:PMC4489264 fatcat:ftzz676gi5celojsthlly2sbpy

Sampling of conformational ensemble for virtual screening using molecular dynamics simulations and normal mode analysis

Gautier Moroy, Olivier Sperandio, Shakti Rielland, Saurabh Khemka, Karen Druart, Divij Goyal, David Perahia, Maria A Miteva
2015 Future Medicinal Chemistry  
Materials \& methods: We assessed our protocols on two well-characterized protein targets showing local active site flexibility, dihydrofolate reductase and large collective movements, CDK2.  ...  Here, we report new fast molecular dynamics-based and normal mode analysis-based protocols combined with conformational pocket classifications to efficiently generate RCEs.  ...  SK and DG were financially supported by ARCUS program of Ministry of Foreign Affairs of France.  ... 
doi:10.4155/fmc.15.150 pmid:26599419 fatcat:f23jonpdnrbzfknpz4djvbytvi

Large-scale comparison of protein essential dynamics from molecular dynamics simulations and coarse-grained normal mode analyses

Aqeel Ahmed, Saskia Villinger, Holger Gohlke
2010 Proteins: Structure, Function, and Bioinformatics  
ACKNOWLEDGMENTS We thank Manuel Rueda (University of Barcelona) for help with the MoDEL database and Daniel Cashman (Heinrich-Heine-University, Düsseldorf) for critically reading the manuscript.  ...  For normal mode-based approaches, this result is helpful in deciding on the number of modes to be considered to explore the essential conformational space.  ...  Furthermore, the calculation of modes only takes seconds for normal-sized proteins and, therefore, can be applied also to large macromolecules.  ... 
doi:10.1002/prot.22841 pmid:20848551 fatcat:lxptpbinbrh4pgvo2zfjndmaqq

Investigation of intrinsic dynamics of enzymes involved in metabolic pathways using coarse-grained normal mode analysis

Sarah M. Meeuwsen, An N. Hodac, Lauren M. Adams, Ryan D. McMunn, Maxwell S. Anschutz, Kari J. Carothers, Rachel E. Egdorf, Peter M. Hanneman, Jonathan P. Kitzrow, Cynthia K. Keonigsberg, Oscar Lopez-Martinez, Paul A. Matthew (+7 others)
2017 Cogent Biology  
In the present study, coarse-grained normal mode analysis was performed to examine the intrinsic dynamic patterns of 24 different enzymes involved in primary metabolic pathways.  ...  Our overall goal is to advance the drug design and screening process, by taking into consideration proteins' intrinsic flexibility.  ...  Earlier studies have shown that low-frequency vibrational modes or normal modes (large fluctuations) of proteins are functionally relevant (Brooks & Karplus, 1983; Go, Noguti, & Nishikawa, 1983; Marques  ... 
doi:10.1080/23312025.2017.1291877 fatcat:l54k4gq5tnb3ta64bdxpr6kq7m

Exploring Binding Mechanisms in Nuclear Hormone Receptors by Monte Carlo and X-ray-derived Motions

Christoph Grebner, Daniel Lecina, Victor Gil, Johan Ulander, Pia Hansson, Anita Dellsen, Christian Tyrchan, Karl Edman, Anders Hogner, Victor Guallar
2017 Biophysical Journal  
To improve sampling of the helix 6-7 loop, we incorporated motion modes based on principal component analysis (PCA) of existing crystal structures of the receptors and applied them to the proteinligand  ...  In the present study, we performed an extensive exploration of the ligand entry mechanism for members of the steroid nuclear hormone receptor family (androgen receptor (AR), estrogen receptor α (ERα),  ...  The large flexibility of the loop connecting helices 6 and 7 is of special importance when studying ligand binding events due to its close vicinity to the ligand binding site.  ... 
doi:10.1016/j.bpj.2017.02.004 pmid:28355542 pmcid:PMC5375144 fatcat:rkwdlrrgkzghrpqxdwrgkhsjei

Characterizing protein motions from structure

Charles C. David, Donald J. Jacobs
2011 Journal of Molecular Graphics and Modelling  
To clarify the extent structure plays in determining protein dynamics, a comparative study is made using three models that characterize native state dynamics of single domain proteins starting from known  ...  Additionally, a mode subspace is constructed from PCA on an exemplar set of myoglobin structures from the Protein Data Bank.  ...  Acknowledgments We wish to thank Dan Farrell and Mike Thorpe for their support of the FRODA software, especially in regards to keeping us current with new features as they are added.  ... 
doi:10.1016/j.jmgm.2011.08.004 pmid:21893421 pmcid:PMC4667955 fatcat:5kc4l5apfzegjkhmtfooeaovhm

Umbrella Visualization: a method of analysis dedicated to glycan flexibility with UnityMol

Camille Besançon, Alexandre Guillot, Sébastien Blaise, Manuel Dauchez, Nicolas Belloy, Jessica Prévoteau-Jonquet, Stéphanie Baud
2019 Methods  
To better decipher the impact of N-glycans, the analysis and visualization of their influence over time on protein structure is a prerequisite.  ...  Because of their high flexibility and the many reactive groups of the glycan chains, studying glycans with in vitro methods is a challenging task.  ...  Indeed, along the trajectories, the glycans don't explore much of the space on the opposite side of this patch.  ... 
doi:10.1016/j.ymeth.2019.07.010 pmid:31302178 pmcid:PMC7128144 fatcat:fdgcs35cbrg3rpwotmkio3hnxe
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