Find Full Paths to Executables

Description

Finds the path to an executable.

Usage

.get.exepath(prg)

Arguments

Value

Returns the absolute path.

Get Web Resource

Description

Gets a web resource.

Usage

.get.url(url, n_tries = 3)

Arguments

Value

Returns the response or an error message.

Residue Found at the Requested Position

Description

Returns the residue found at the requested position.

Usage

aa.at(at, target, uniprot = TRUE)

Arguments

Details

Please, note that when uniprot is set to FALSE, target can be the string returned by a suitable function, such as get.seq or other.

Value

Returns a single character representing the residue found at the indicated position in the indicated protein.

Author(s)

Juan Carlos Aledo

See Also

is.at(), aa.comp()

Examples

## Not run: aa.at(28, 'P01009')

Amino Acid Composition

Description

Returns a table with the amino acid composition of the target protein.

Usage

aa.comp(target, uniprot = TRUE, reference = 'human', init = FALSE)

Arguments

Value

Returns a list where the first element is a dataframe with the observed and expected frequencies for each amino acid, the second element is the result of the Chi-squared test. In addition, a plot to reflect potential deviations from the reference standard composition is shown.

Author(s)

Juan Carlos Aledo

See Also

is.at(), renum.pdb(), renum.meto(), renum(), aa.at()

Examples

aa.comp('MPSSVSWGILLLAGLCCLVPVSLAEDPQGDAAQK', uniprot = FALSE)

Import a Protein Sequence from a Database

Description

Imports a protein sequence from a selected database.

Usage

get.seq(id, db = 'uniprot', as.string = TRUE)

Arguments

Details

MetOSite uses the same type of protein ID than UniProt.

Value

Returns a protein sequence either as a character vector or a as a character string.

Examples

get.seq('P01009')

Check that Internet Resource Work Properly and Fail Gracefully When Not

Description

Checks that internet resource works properly and fail gracefully when not.

Usage

gracefully_fail(call, timeout = 10,  ...)

Arguments

Details

To be used as an ancillary function.

Value

The response object or NULL when the server does not respond properly.

Author(s)

thefactmachine

References

https://gist.github.com/thefactmachine/18279b7796c0836d9188

Examples

gracefully_fail("http://httpbin.org/delay/2")

Human MetO sites oxidized by hydrogen peroxide treatment.

Description

A dataset containing data regarding human MetO sites oxidized by H2O2.

Usage

hmeto

Format

A data frame with 4472 rows and 15 variables:

prot_id

UniProt ID of the oxidized protein

prot_name

the protein's name

met_pos

the position of the MetO site in the primary structure

met_vivo_vitro

conditions under which the oxidation experiment was carried out

MetOsites

array with all the sites oxidized in that protein

site_id

primary key identifying the site

positive

sequence environment of the MetO site

control

sequence environment of a non oxidized Met from the same protein

IDP

Intrinsically Disordered Proteins, 0: the protein is not found in DisProt; 1: the protein contains disordered regions; 2: the protein may contain disordered regions but the experimental evidences are ambiguous

IDR

Intrinsically Disordered Region, TRUE: the MetO site belong to the IDR, FALSE: the MetO site doesn't belong to the IDR

abundance

protein abundance, in ppm

N

protein length, in number of residues

met

number of methionine residues

fmet

relative frequency of Met in that protein

prot_vivo_vitro

whether the protein has been described to be oxidized in vivo, in vitro or under both conditions

Source

https://metosite.uma.es/

Check Residue a Fixed Position

Description

Checks if a given amino acid is at a given position.

Usage

is.at(at, target, aa = 'M', uniprot = TRUE)

Arguments

Details

Please, note that when uniprot is set to FALSE, target can be the string returned by a suitable function, such as get.seq or other.

Value

Returns a boolean. Either the residue is present at that position or not.

Author(s)

Juan Carlos Aledo

See Also

aa.at(), aa.comp()

Examples

## Not run: is.at(28, 'P01009', 'Q')

List Proteins Found in MetOSite Matching a Keyword

Description

Lists proteins found in MetOSite with names matching the keyword.

Usage

meto.list(keyword)

Arguments

Value

This function returns a dataframe with the uniprot id, the protein name and the species, for those proteins present into MetOSite whose name contains the keyword.

Author(s)

Juan Carlos Aledo

References

Valverde et al. 2019. Bioinformatics 35:4849-4850 (PMID: 31197322)

See Also

meto.search(), meto.scan()

Examples

meto.list('inhibitor')

Scans a Protein in Search of MetO Sites

Description

Scans a given protein in search of MetO sites.

Usage

meto.scan(up_id, report = 1)

Arguments

Details

When the 'report' parameter has been set to 1, this function returns a brief report providing the position, the function category and literature references concerning the residues detected as MetO, if any. If we wish to obtain a more detailed report, the option should be: report = 2. Finally, If we want a detailed and printable report (saved in the current directory), we should set report = 3

Value

This function returns a report regarding the MetO sites found, if any, in the protein of interest.

Author(s)

Juan Carlos Aledo

References

Valverde et al. 2019. Bioinformatics 35:4849-4850 (PMID: 31197322)

See Also

meto.search(), meto.list()

Examples

meto.scan('P01009')

Search for Specific MetO Sites

Description

Searches for specific MetO sites filtering MetOSite according to the selected criteria.

Usage

meto.search(highthroughput.group = TRUE,
                   bodyguard.group = TRUE,
                   regulatory.group = TRUE,
                   gain.activity = 2, loss.activity = 2, gain.ppi = 2,
                   loss.ppi = 2, change.stability = 2, change.location = 2,
                   organism = -1, oxidant = -1)

Arguments

Details

Note that all the arguments of this function are optional. We only pass an argument to the function when we want to use that parameter to filter. Thus, meto.search() will return all the MetO sites found in the database MetOSite.

Value

This function returns a dataframe with a line per MetO site.

Author(s)

Juan Carlos Aledo

References

Valverde et al. 2019. Bioinformatics 35:4849-4850 (PMID: 31197322)

See Also

meto.scan(), meto.list()

Examples

meto.search(organism = 'Homo sapiens', oxidant = 'HClO')

Compute Euclidean Distances

Description

Computes the pairwise distance matrix between two sets of points

Usage

pairwise.dist(a, b, squared = TRUE)

Arguments

Value

Euclidean distance matrix (NxM). An attribute "squared" set to the value of param squared is provided.

Examples

pairwise.dist(matrix(1:9, ncol = 3), matrix(9:1, ncol = 3))

Compute Distances to the Closest Aromatic Residues

Description

Computes distances to the closest aromatic residues.

Usage

saro.dist(pdb, threshold = 7, rawdata = FALSE)

Arguments

Details

For each methionyl residue this function computes the distances to the closest aromatic ring from Y, F and W. When that distance is equal or lower to the threshold, it will be computed as a S-aromatic motif.

Value

The function returns a dataframe with as many rows as methionyl residues are found in the protein. The distances in ångströms to the closest tyrosine, phenylalanine and triptophan are given in the columns, as well as the number of S-aromatic motifs detected with each of these amino acids. Also a raw distance matrix can be provided.

Author(s)

Juan Carlos Aledo

References

Reid, Lindley & Thornton, FEBS Lett. 1985, 190:209-213.

See Also

saro.motif(), saro.geometry()

Examples

## Not run: saro.dist('1CLL')

Compute Geometric Parameters of S-Aromatic Motifs

Description

Computes distances and angles of S-aromatic motifs.

Usage

saro.geometry(pdb, rA, chainA = 'A', rB, chainB = 'A')

Arguments

Details

The distance between the delta sulfur atom and the centroid of the aromatic ring is computed, as well as the angle between this vector and the one perpendicular to the plane containing the aromatic ring. Based on the distance (d) and the angle (theta) the user decide whether the two residues are considered to be S-bonded or not (usually when d < 7 and theta < 60º).

Value

The function returns a dataframe providing the coordinates of the sulfur atom and the centroid (centroids when the aromatic residue is tryptophan), as well as the distance (ångströms) and the angle (degrees) mentioned above.

Author(s)

Juan Carlos Aledo

References

Reid, Lindley & Thornton, FEBS Lett. 1985, 190, 209-213.

See Also

saro.motif(), saro.dist()

Examples

## Not run: saro.geometry('1CLL', rA = 141, rB = 145)

Search for S-Aromatic Motifs

Description

Searches for S-aromatic motifs in proteins.

Usage

saro.motif(pdb, threshold = 7, onlySaro = TRUE)

Arguments

Details

For each methionyl residue taking place in a S-aromatic motif, this function computes the aromatic residues involved, the distance between the delta sulfur and the aromatic ring's centroid, as well as the angle between the sulfur-aromatic vector and the normal vector of the plane containing the aromatic ring.

Value

The function returns a dataframe reporting the S-aromatic motifs found for the protein of interest.

Author(s)

Juan Carlos Aledo

References

Reid, Lindley & Thornton, FEBS Lett. 1985, 190, 209-213.

See Also

saro.dist(), saro.geometry()

Examples

## Not run: saro.motif('1CLL')

Compute Cross Product

Description

Computes the cross product of two vectors in three-dimensional euclidean space.

Usage

xprod(...)

Arguments

Details

For each methionyl residue taking place in a S-aromatic motif, this function computes the aromatic residue involved, the distance between the delta sulfur and the aromatic ring's centroid, as well as the angle between the sulfur-aromatic vector and the normal vector of the plane containing the aromatic ring.

Value

This function returns a vector that is orthogonal to the plane containing the two vector used as arguments.

Author(s)

Juan Carlos Aledo

Examples

xprod(c(1,1,1), c(1,2,1))