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CMView: Interactive contact map visualization and analysis

C. Vehlow, H. Stehr, M. Winkelmann, J. M. Duarte, L. Petzold, J. Dinse, M. Lappe
2011 Bioinformatics  
We developed a tool called CMView which integrates rich contact map analysis with 3D visualization using PyMol.  ...  Our tool provides functions for contact map calculation from structure, basic editing, visualization in contact map and 3D space and structural comparison with different built-in alignment methods.  ...  Bolser and Ioannis Filippis for helpful comments and suggestions. Funding: Max Planck Society. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btr163 pmid:21471016 fatcat:mqcl6gpa5faitnulkwbxygfjau

Available Instruments for Analyzing Molecular Dynamics Trajectories

I. V. Likhachev, N. K. Balabaev, O. V. Galzitskaya
2016 Open Biochemistry Journal  
Based on the definition, in a text format trajectory files are characterized by their simplicity and uselessness.  ...  The performance of these programs, usefulness for analyses of molecular dynamics trajectories, strong and weak aspects are discussed. © Likhachev et al.; Licensee Bentham Open.  ...  the Ministry of Education and Science of the Republic of Kazakhstan for NKB and OVG.  ... 
doi:10.2174/1874091x01610010001 pmid:27053964 pmcid:PMC4797681 fatcat:qogx6q4upjdqrgfd4nvq7vssim

CMWeb: an interactive on-line tool for analysing residue-residue contacts and contact prediction methods

D. Kozma, I. Simon, G. E. Tusnady
2012 Nucleic Acids Research  
The server can be used to visualize contact maps, to link contacts and to show them both in 3D structures and in multiple sequence alignments and to calculate various statistics on contacts.  ...  Moreover, we have implemented five contact prediction methods in the CMWeb server to visualize the predicted and real RR contacts in one contact map.  ...  The most recent contact map viewers is the CMView (13) program using PyMol (14) for visualizing the 3D structures.  ... 
doi:10.1093/nar/gks488 pmid:22669913 pmcid:PMC3394325 fatcat:b623yddgs5hzpdnnrmq4jxy3bm

Visualization of anisotropic contact potentials within protein structures

Corinna Vehlow, Bernhard Preim, Michael Lappe
2011 2011 IEEE Symposium on Biological Data Visualization (BioVis).  
The Contact Geometry Analysis Plugin (CGAP) (for CMView) we developed allows incorporation of geometric orientation propensities into the process of interactive protein modeling and can be used for the  ...  For this purpose, two novel visualization principles will be introduced. The first visualization illustrates anisotropic residuedependent contact density potentials in the form of a map projection.  ...  Two-dimensional visualizations are more appropriate for interactive analysis and assignment. Hence, map projections will be used to visualize the propensities within a defined shell.  ... 
doi:10.1109/biovis.2011.6094045 dblp:conf/biovis/VehlowPL11 fatcat:qsubl5lafbfnloco6gb64vgkaq

RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps

J. E. Chen, C. C. Huang, T. E. Ferrin
2014 Bioinformatics  
An interactive utility, RRDistMaps, visualizes conformational changes, both local (e.g. binding-site residues) and global (e.g. hinge motion), between unbound and bound proteins through distance patterns  ...  An interactive utility, RRDistMaps visualizes conformational changes, both local (e.g., binding-site residues), and global (e.g., hinge motion), between unbound and bound proteins through distance patterns  ...  Funding: This work was supported by NIH grant NIGMS P41-GM103311 and the UCSF-Lowell Summer Internship Program. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btu841 pmid:25540183 pmcid:PMC4410660 fatcat:aaofce2cfzfojgv5ht6skaf5iy

NAPS: Network Analysis of Protein Structures

Broto Chakrabarty, Nita Parekh
2016 Nucleic Acids Research  
Visual analysis of interacting domains and protein chains, and shortest path lengths between pair of residues are additional features that aid in functional analysis.  ...  We have developed a web server for network based analysis of protein structures, NAPS, that facilitates quantitative and qualitative (visual) analysis of residueresidue interactions in: single chains,  ...  Standalone programs such as SeqX (18) , Protmap2D (19) and CMview (20) allow construction and basic analysis of contact maps.  ... 
doi:10.1093/nar/gkw383 pmid:27151201 pmcid:PMC4987928 fatcat:pgnzugk5lbhg7f4yzjs5pocdoy

RNAmap2D – calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures

Michal J Pietal, Natalia Szostak, Kristian M Rother, Janusz M Bujnicki
2012 BMC Bioinformatics  
Results: We developed RNAmap2D, a platform-independent software tool for calculation, visualization and analysis of contact and distance maps for nucleic acid molecules and their complexes with proteins  ...  Molecular structures, however, can be represented as 2D maps of interactions between the individual residues, which are easier to visualize and compare, and which can be reconverted to 3D structures with  ...  The authors also thank Anna Philips for help in analyzing structures containing ligands and ions and with nucleotide modifications lists encoded within the RNAmap2D.  ... 
doi:10.1186/1471-2105-13-333 pmid:23259794 pmcid:PMC3556492 fatcat:ek2xysgfvrhqtb7yvgdwqhfviy

FoldSynth: Interactive 2D/3D Visualisation Platform for Molecular Strands [article]

Stephen Todd, Peter Todd, Frederic Fol Leymarie, William Latham, Lawrence A. Kelley, Michael Sternberg, Jim Hugues, Stephen Taylor
2015 Eurographics Workshop on Visual Computing for Biomedicine  
FoldSynth is an interactive platform designed to help understand the characteristics and commonly used visual abstractions of molecular strands with an emphasis on proteins and DNA.  ...  As well as more conventional raster plots, contact maps can be shown with vectors representing the grouping of contacts as secondary structures.  ...  For example, the CMView (or Contact Map View) package provides only the visualisation and analysis of static results [V * 11].  ... 
doi:10.2312/vcbm.20151207 dblp:conf/vcbm/ToddTLLKSHT15 fatcat:phbh7jnwizewfcidf4kb2ypjga

Defining an Essence of Structure Determining Residue Contacts in Proteins

R. Sathyapriya, Jose M. Duarte, Henning Stehr, Ioannis Filippis, Michael Lappe, Ruth Nussinov
2009 PLoS Computational Biology  
We selected a test-set of 12 protein structures from the four major SCOP fold classes and performed our reconstruction analysis.  ...  We present, for the first time, a rational strategy to derive a structural essence of residue contacts and provide an estimate of the size of this minimal subset.  ...  The contacts are visualized in a contact map with CMView [CMView: Interactive Contact Map Visualization and Analysis. http://www.molgen.mpg.de/,lappe/cmview/].  ... 
doi:10.1371/journal.pcbi.1000584 pmid:19997489 pmcid:PMC2778133 fatcat:ycvziysu45b3jihpyp7hjqashq

Identification of Conformational B-cell Epitopes in Diphtheria Toxin at Varying Temperatures Using Molecular Dynamics Simulations

S Ghaderi, M R Bozorgmehr, M Ahmadi, Sh Tarahomjoo
2021 Archives of Razi Institute  
Furthermore, the tertiary structure of the DT was compared at different temperatures using the contact map.  ...  In addition, amino acids D68, G128, G171, C186, and K534-S535 at 27˚C and 37˚C, as well as amino acids G26, P38, S291, T267, H384, A356, and V518 at 47˚C showed higher root mean square fluctuation values  ...  1.1.1) which is an interactive contact map visualization tool (Vehlow et al., 2011) .  ... 
doi:10.22092/ari.2019.127251.1377 pmid:33403838 pmcid:PMC8410147 fatcat:cbrljitl4fdmpi4pu4f3lfpe5y

Structural Comparison of the SARS CoV 2 Spike Protein Relative to Other Human-Infecting Coronaviruses

Marni E. Cueno, Kenichi Imai
2021 Frontiers in Medicine  
Tm scores, and contact mapping were all performed.  ...  and SARS2.  ...  Moreover, CMView applet (Contact type: Cα; Distance cut-off: 8.0; Needleman-Wunsch alignment) was used to establish protein contact map of both the model and crystal in order to determine common contact  ... 
doi:10.3389/fmed.2020.594439 pmid:33585502 pmcid:PMC7874069 fatcat:fxucvwdfn5agzhbcqspmhbxlca

HIV-1 matrix trimerization-impaired mutants are rescued by matrix substitutions that enhance envelope glycoprotein incorporation

Philip R. Tedbury, Mariia Novikova, Ayna Alfadhli, Yuta Hikichi, Ioannis Kagiampakis, Vineet N. KewalRamani, Eric Barklis, Eric O. Freed
2019 Journal of Virology  
Our data highlight the significance of the trimer interface of the MA domain of Gag as a critical site of protein-protein interaction during HIV-1 assembly, and establish the functional importance of trimeric  ...  The compensatory mutations located within or near the trimer interface restored Env incorporation and particle infectivity, and permitted replication in culture.  ...  Thr69 (red) and Leu74 (purple) are present at the trimer interface and have previously been shown to impair MA trimerization FIG 2 2 Contact map analysis for MA trimer.  ... 
doi:10.1128/jvi.01526-19 pmid:31619553 pmcid:PMC6912099 fatcat:ixj43i7wlfgevpf2zwbbd3mdsy

Pressure and Chemical Unfolding of an α-Helical Bundle Protein: The GH2 Domain of the Protein Adaptor GIPC1

Cécile Dubois, Vicente J. Planelles-Herrero, Camille Tillatte-Tripodi, Stéphane Delbecq, Léa Mammri, Elena M. Sirkia, Virginie Ropars, Christian Roumestand, Philippe Barthe
2021 International Journal of Molecular Sciences  
Whatever the perturbation used, the loss of secondary and tertiary contacts within the protein scaffold is almost simultaneous.  ...  Native contact maps were obtained by using software CMView (http://www.bioinfor matics.org/cmview/; accessed on 25 March 2020) with a threshold of 9 Å around the Cα of each residue, using the best structure  ...  (B) Visualization of the probabilities of contact on ribbon representations of GIPC1-GH2 at 20 °C and at 2.4, 2.6, 2.8, and 3 M urea, as indicated.  ... 
doi:10.3390/ijms22073597 pmid:33808390 fatcat:vnu2wujafzdqdcu3yte2yxg3pm

Aspergillus Oryzae S2 α-Amylase Domain C Involvement in Activity and Specificity: In Vivo Proteolysis, Molecular and Docking Studies

Mouna Sahnoun, Sonia Jemli, Sahar Trabelsi, Leila Ayadi, Samir Bejar, Luis Menéndez-Arias
2016 PLoS ONE  
The contact map analysis and the docking studies strongly suggested a higher activity and substrate binding affinity for AmyB than AmyA which was previously experimentally exhibited.  ...  The amino-acid sequence analysis revealed aY371 potential chymotrypsin cleaving site, likely to be the AmyB C-Terminal end and two other potential sites at Y359, and F379.  ...  Salma Karray for her constructive proofreading and language polishing services. The authors would also like to thank the reviewers for their efforts during the revision of the present manuscript.  ... 
doi:10.1371/journal.pone.0153868 pmid:27101008 pmcid:PMC4839703 fatcat:henffjxbvjbg7jq2n6ocds5pdi

Structure elements can be predicted using the contact volume among protein residues

Yasumichi Takase, Yoichi Yamazaki, Yugo Hayashi, Sachiko Toma-Fukai, Hironari Kamikubo
2021 Biophysics and Physicobiology  
However, the comprehensive Ala-insertion mutation analysis is a time- and cost-consuming process and only a set of the DHFR structure elements have been reported so far.  ...  We introduced a simple and effective parameter: the overlapped contact volume (CV) among the residues and calculated the CV along the DHFR sequence using the crystal structure.  ...  Author Contributions Y.T. and H.K. conceived the project and designed the research. Y.T., Y.Y., Y.H., S.T.F., and H.K. performed the research. Y.T. and H.K. wrote the paper.  ... 
doi:10.2142/biophysico.bppb-v18.006 pmid:33954082 pmcid:PMC8049775 fatcat:6kik7rcjgjdhfca6b3n7ahxn4i
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