MD Analysis of Residue Properties Using Structural Alphabets

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Documentation for package ‘MDaRes’ version 0.0.2

• DESCRIPTION file
• Package NEWS
• Package README

Help Pages

add_active_site	Retrieve and Format Active Site Annotations from UniProt
add_binding_site	Retrieve and Format Ligand Binding Site Annotations from UniProt
add_disulfide_bond	Retrieve and Format Disulfide Bond Annotations from UniProt
add_domain	Retrieve and Format Domain Annotations from UniProt
add_glycosilation	Retrieve and Format Glycosylation Annotations from UniProt
add_lipidation	Retrieve and Format Lipidation Annotations from UniProt
add_location	Retrieve and Format Location Annotations from UniProt
add_modified_residue	Retrieve and Format Modified Residue Annotations from UniProt
add_molecule_processing	Retrieve and Format Molecule Processing Annotations from UniProt
add_motive	Retrieve and Format Motif Annotations from UniProt
add_secondary_structure	Retrieve and Format Secondary Structure Annotations from UniProt
add_uniprot_annotation	Retrieve and Merge UniProt Annotations
add_variants	Retrieve and Format Protein Variants from UniProt
colnames_substring	Extract Substring from Column Names
create_annotation_df	Retrieve UniProt Protein Sequence and Format as Dataframe
do_freq_diff_plot	Save frequency-difference plot to PNG
do_freq_plot	Generate Frequency Profile Plot and Save to PNG
do_MI_plot	Generate Mutual Information Matrix Plot and Save to PNG
do_shannon_entropy_diff_plot	Save Shannon Entropy Difference Plot to PNG
do_shannon_entropy_plot	Generate Shannon Entropy Plot and Save to PNG
entropy_visualization	Visualize Shannon Entropy on a Protein Structure
freq_diff_plot	Plot Structural Frequency Differences
freq_plot	Plot Frequency Profile
get_res_numbering	Retrieve Residue Numbering from Encoded Trajectory
import_SA	Import Structural Alphabet from PDB Files
MImat	Compute Mutual Information Matrix
MI_plot	Plot Mutual Information Matrix
MI_ranking_couple	Rank Residues Based on Mutual Information
MI_ranking_median	Rank Mutual Information by Median and Collectivity
nMImat	Compute Normalized Mutual Information Matrix
SA_encoding	Encode an MD Trajectory Using a Structural Alphabet (C++ backend)
shannon_entropy	Compute Shannon Entropy and Frequency Distribution
shannon_entropy_diff_plot	Plot Shannon Entropy Difference
shannon_entropy_plot	Plot Shannon Entropy
shannon_ranking	Rank Fragments by Shannon Entropy
total_ranking	Merge Shannon Entropy and MI Rankings