Documentation

The ptm package, written to assist the study of protein post-translational modifications, consists of sets of functions that can be grouped, according to their functionality, into the following categories:

• Functions exploring data from MetOSite (a methionine sulfoxidation database).
• Functions integrating data from other main PTM databases.
• Functions to study S-aromatic motifs.
• Functions to analyze sequence environment.
• Functions to handle sequences from different databases.
• Evolutionary analysis tools.
• GO network analysis.
• Ancillary tools dealing with PDB files.
• Functions to explore protein surfaces.
• Functions to explore thermodynamic stability.
• Tools for sequence re-numbering.
• Functions related to inter-atomic and inter-residue distances.
• Miscellanea functions related to protein properties.
• Functions related to data visualization.

Major functions are listed below with links to further documentation that includes example code and results.

Note that you can also get help on any particular function by using the command ?function or help(function) (e.g. help(meto.search)).

We also distribute a number of extended ptm vignettes that provide worked examples of using ptm to perform a particular type of analysis. Currently available vignettes include:

• S-Aromatic Motifs and Calmodulin
• Exploring MetO Sequence Environments
• Regulatory and Non-Regulatory Phosphoserines

Help topics

Exploring data from MetOSite

• meto.search: Searchs for Specific MetO Sites.
• meto.scan: Scans a Protein in Search of MetO Sites.
• meto.list: Lists Proteins Found in MetOSite Matching a Keyword.

Integrating data from other main PTM databases

• p.scan: Scans a Protein in Search of Phosphosites.
• ac.scan: Scans a Protein in Search of Acetylation Sites.
• me.scan: Scans a Protein in Search of Methylation Sites.
• ub.scan: Scans a Protein in Search of Ubiquitination Sites.
• su.scan: Scans a Protein in Search of Sumoylation Sites.
• gl.scan: Scans a Protein in Search of OGlcNAc Sites.
• sni.scan: Scans a Protein in Search of S-nitrosylation Sites.
• ni.scan: Scans a Protein in Search of Nitration Sites.
• ptm.scan: Scans a Protein in Search of PTM Sites.
• reg.scan: Scans a Protein in Search of Regulatory PTM Sites.
• dis.scan: Scans a Protein in Search of Disease-Related PTM Sites.

Functions to study S-aromatic motifs

• saro.motif: Searchs for S-Aromatic Motifs in Proteins.
• saro.gemometry: Computes Distances and Angles of S-Aromatic Motifs.
• saro.dist: Computes Distances to the Closest Aromatic Residues and the Number of S-Aromatic Motifs.

Functions to analyse sequence environments

• env.extract: Extracts the Sequence Environment Around a Given Position.
• env.matrices: Provides the Frequencies of Each Amino Acid Within the Environment.
• env.Ztest: Searches for Amino Acids Either Overrepresented or Avoided at Given Positions Within a Sequence Environment.
• env.plot: Plots the Z Statistics at Each Position Within the Environment for the Requested Amino Acid.

Handling sequences from different databases

• get.seq: Imports a Protein Sequence from a Database.
• prot2codon: Finds the Coding Triplets for a Given Protein.
• id.mapping: Identifier Mapping.
• id.features: Features Related to the Protein Entry.
• species.mapping: Maps Protein ID to Species.

Evolutionary analysis tools

• msa: Multiple Sequence Alignment.
• custom.aln: Downloads and Aligns Orthologous Sequences.
• list.hom: Searchs Homologous Entries.
• parse.hssp: Parses a HSSP File to Return Dataframes.
• get.hssp: Gets a HSSP File.
• shannon: Computes Shannon Entropy for Amino Acid and Codon Sites.
• site.type: Computes Shannon Entropy and Sort out the Sites.

GO network and enrichment analyses

• search.go: Searches a Simple User Query.
• term.go: Gets Core Information About the GO Term of Interest.
• get.go: Gets the Gene Ontology Annotations for a Given Protein.
• bg.go: Searches GO Terms for Background Set.
• hdfisher.go: Carries Out an Enrichment Fisher’s Test Using a Hypothesis-Driven Approach.
• gorilla: Performs GO Terms Enrichment Analyses.
• net.go: Explores the Relationship Among Proteins from a Given Set.

Ancillary tools dealing with PDB files

• pdb.quaternary: Determines the Subunit Composition of a Given Protein.
• pdb.chain: Downloads a PDB File and Splits it to Provide a File by Chain.
• uniprot2pdb: Returns the PDB and Chain IDs of the Provided Protein.
• pdb2uniprot: Returns the UniProt ID of a Given Chain Within a PDB Structure.
• pdb.res: Checks Whether or Not a Given Residue is Resolved in the PDB Structure.
• pdb.pep: Checks Whether a Given Oligopeptide is Resolved in the PDB.
• compute.dssp: Computes and Returns a DSSP File.
• parse.dssp: Parses a DSSP File to Return a Dataframe.
• mkdssp: Computes DSSP Files Using an In-House Version of the DSSP Software.

Functions to explore protein surfaces.

• acc.dssp: Computes Residue Accessibility and SASA.
• get.area: Atomic Solvation Energies.
• atom.dpx: Atom Depth Analysis.
• res.dpx: Residue Depth Analysis.
• stru.part: Partition of Structural Regions.

Functions to explore thermodynamic stability.

• imutant: Computes Changes in Stability Using a Machine-Learning Approach.
• foldx.mut: Computes Changes in Stability Using a Force-Field Approach.
• ddG.profile: Represents the Sensitivity of a Given Position to Changes in Stability.
• ddG.ptm: Computes Changes in Stability After PTM.

Tools for sequence re-numbering

• aa.at: Returns the Residue Found at the Requested Position.
• is.at: Checks if a Given Amino Acid is at a Given Position.
• renum.pdb: Renumerates Residue Position of a PDB Sequence to Match the Corresponding UniProt Sequence.
• renum.meto: Renumerates Residue Position of a MetOSite Sequence to Match the Corresponding UniProt Sequence.
• renum: Renumerates Residue Position.
• aa.comp: Returns a Table with the Amino Acid Composition of the Target Protein.

Functions related to inter-atomic and inter-residue distances

• res.dist: Computes the Euclidean Distance Between Two Given Residues.
• dist2closest: Computes the Distance to the Closest Amino Acid of the Indicated Type.
• ball: Finds the Atoms Within a Sphere with the Indicated Center and Radius.
• pairwise.dist: Computes the Pairwise Distance Matrix Between Two Sets of Points.

Miscellanea functions related to protein properties

• abundance: Returns Data Regarding the Abundance of a Given Protein.

Data visualization

• env.plot: Plots the Z Statistics at Each Position Within the Environment for the Requested Amino Acid.
• ptm.plot: Plots Values of Property and PTM Sites Along the Protein Sequence.
• ddG.profile: Represents the Sensitivity of a Given Position to Changes in Stability.
• site.type: Computes Shannon Entropy and Sort out the Sites.

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