Package: MDaRes 0.0.2

MDaRes: MD Analysis of Residue Properties Using Structural Alphabets

Analyze molecular dynamics (MD) simulation data using structural alphabets. Protein local conformations from molecular simulations are encoded in a compressed string representation. Residue-level UniProt annotations can be directly retrieved. Comparative analysis tools are available to investigate conformational variability, coordinated motions, and differences between systems (e.g. wild-type vs mutant; bound vs unbound). Methodological details for the structural alphabet analysis can be found in Pandini et al. (2013) <doi:10.1093/bioinformatics/btt326>.

Authors:Nancy D'Arminio [aut], Anna Marabotti [aut], Alessandro Pandini [aut, cph, cre]

MDaRes_0.0.2.tar.gz
MDaRes_0.0.2.zip(r-4.7-x86_64)MDaRes_0.0.2.zip(r-4.7-arm64)MDaRes_0.0.2.zip(r-4.6-x86_64)MDaRes_0.0.2.zip(r-4.6-arm64)MDaRes_0.0.2.zip(r-4.5-x86_64)
MDaRes_0.0.2.tgz(r-4.6-x86_64)MDaRes_0.0.2.tgz(r-4.6-arm64)MDaRes_0.0.2.tgz(r-4.5-x86_64)MDaRes_0.0.2.tgz(r-4.5-arm64)
MDaRes_0.0.2.tar.gz(r-4.7-arm64)MDaRes_0.0.2.tar.gz(r-4.7-x86_64)MDaRes_0.0.2.tar.gz(r-4.6-arm64)MDaRes_0.0.2.tar.gz(r-4.6-x86_64)
MDaRes_0.0.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MDaRes/json (API)

# Install 'MDaRes' in R:
install.packages('MDaRes', repos = c('https://alepandini.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

cpp

1.07 score 1.2k downloads 32 exports 201 dependencies

Last updated from:4f28c3367a. Checks:15 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK289
linux-devel-x86_64OK350
source / vignettesOK314
linux-release-arm64OK282
linux-release-x86_64OK353
macos-release-arm64OK348
macos-release-x86_64OK454
macos-oldrel-arm64OK284
macos-oldrel-x86_64OK483
windows-devel-arm64OK525
windows-devel-x86_64OK366
windows-release-arm64OK516
windows-release-x86_64OK287
windows-oldrel-x86_64OK322
wasm-releaseOK220

Exports:add_active_siteadd_binding_siteadd_disulfide_bondadd_domainadd_glycosilationadd_lipidationadd_locationadd_modified_residueadd_molecule_processingadd_motiveadd_secondary_structureadd_uniprot_annotationadd_variantsdo_freq_diff_plotdo_freq_plotdo_MI_plotdo_shannon_entropy_diff_plotdo_shannon_entropy_plotentropy_visualizationfreq_diff_plotfreq_plotimport_SAMI_plotMI_ranking_coupleMI_ranking_medianMImatSA_encodingshannon_entropyshannon_entropy_diff_plotshannon_entropy_plotshannon_rankingtotal_ranking

Dependencies:abindade4airralakazamapeaskpassbackportsbase64encBHbio3dBiocGenericsBiocParallelBiostringsbitbit64bitopsblobbootbroombslibcachemcallrcarcarDatacellrangercigarilloclassclicliprclustercodetoolscolorspaceconflictedcorrplotcowplotcpp11crayoncrosstalkcurldata.tabledata.treeDBIdbplyrDerivDescToolsdigestdoBydplyrdtplyre1071evaluateExactexpmfarverfastmapfontawesomeforcatsforecastformatRFormulafracdifffsfutile.loggerfutile.optionsgarglegenericsGenomicAlignmentsGenomicRangesggplot2ggpubrggrepelggsciggsignifgldgluegoogledrivegooglesheets4gprofiler2gridExtragtablehavenhighrhmshtmltoolshtmlwidgetshttridsigraphIRangesisobandjquerylibjsonliteknitrkohonenlabelinglambda.rlaterlatticelazyevallifecyclelme4lmomlmtestlubridatemagickmagrittrMASSMatrixMatrixModelsmemoisemgcvmimeminqamodelrmvtnormnetworkD3nlmenloptrnnetnumDerivopensslotelpbkrtestpillarpixmappkgconfigplotlyplyrpolynomprettyunitsprocessxprogresspromisesproxypspurrrqdapRegexquantregR6raggrappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreadrreadxlreformulasrematchrematch2reprexRhtslibrlangrmarkdownrootSolveRsamtoolsrstatixrstudioapirvestS4VectorsS7sassscalessegmentedselectrSeqinfoseqinrsnowSOMMDspSparseMstringistringrsurvivalsyssystemfontstextshapingtibbletidyrtidyselecttidyversetimechangetimeDatetinytextzdbUniprotRurcautf8uuidvctrsviridisLitevroomwithrxfunxml2XVectoryamlzoo

Readme and manuals

Help Manual

Help pageTopics
Retrieve and Format Active Site Annotations from UniProtadd_active_site
Retrieve and Format Ligand Binding Site Annotations from UniProtadd_binding_site
Retrieve and Format Disulfide Bond Annotations from UniProtadd_disulfide_bond
Retrieve and Format Domain Annotations from UniProtadd_domain
Retrieve and Format Glycosylation Annotations from UniProtadd_glycosilation
Retrieve and Format Lipidation Annotations from UniProtadd_lipidation
Retrieve and Format Location Annotations from UniProtadd_location
Retrieve and Format Modified Residue Annotations from UniProtadd_modified_residue
Retrieve and Format Molecule Processing Annotations from UniProtadd_molecule_processing
Retrieve and Format Motif Annotations from UniProtadd_motive
Retrieve and Format Secondary Structure Annotations from UniProtadd_secondary_structure
Retrieve and Merge UniProt Annotationsadd_uniprot_annotation
Retrieve and Format Protein Variants from UniProtadd_variants
Extract Substring from Column Namescolnames_substring
Retrieve UniProt Protein Sequence and Format as Dataframecreate_annotation_df
Save frequency-difference plot to PNGdo_freq_diff_plot
Generate Frequency Profile Plot and Save to PNGdo_freq_plot
Generate Mutual Information Matrix Plot and Save to PNGdo_MI_plot
Save Shannon Entropy Difference Plot to PNGdo_shannon_entropy_diff_plot
Generate Shannon Entropy Plot and Save to PNGdo_shannon_entropy_plot
Visualize Shannon Entropy on a Protein Structureentropy_visualization
Plot Structural Frequency Differencesfreq_diff_plot
Plot Frequency Profilefreq_plot
Retrieve Residue Numbering from Encoded Trajectoryget_res_numbering
Import Structural Alphabet from PDB Filesimport_SA
Plot Mutual Information MatrixMI_plot
Rank Residues Based on Mutual InformationMI_ranking_couple
Rank Mutual Information by Median and CollectivityMI_ranking_median
Compute Mutual Information MatrixMImat
Compute Normalized Mutual Information MatrixnMImat
Encode an MD Trajectory Using a Structural Alphabet (C++ backend)SA_encoding
Compute Shannon Entropy and Frequency Distributionshannon_entropy
Plot Shannon Entropy Differenceshannon_entropy_diff_plot
Plot Shannon Entropyshannon_entropy_plot
Rank Fragments by Shannon Entropyshannon_ranking
Merge Shannon Entropy and MI Rankingstotal_ranking