R: Ensemble Normal Mode Analysis with All-Atom ENM

aanma.pdbs {bio3d} | R Documentation

## Ensemble Normal Mode Analysis with All-Atom ENM

### Description

Perform normal mode analysis (NMA) on an ensemble of aligned protein structures using all-atom elastic network model (aaENM).

### Usage

    ## S3 method for class 'pdbs'
    aanma(pdbs, fit = TRUE, full = FALSE, subspace = NULL,
      rm.gaps = TRUE, ligand = FALSE, outpath = NULL, gc.first = TRUE,
      ncore = NULL, ...)

### Arguments

`pdbs` | an ‘pdbs’ object as obtained from `read.all`.
`fit` | logical, if TRUE C-alpha coordinate based superposition is performed prior to normal mode calculations.
`full` | logical, if TRUE return the complete, full structure, ‘nma’ objects.
`subspace` | number of eigenvectors to store for further analysis.
`rm.gaps` | logical, if TRUE obtain the hessian matrices for only atoms in the aligned positions (non-gap positions in all aligned structures). Thus, gap positions are removed from output.
`ligand` | logical, if TRUE ligand molecules are also included in the calculation.
`outpath` | character string specifing the output directory to which the PDB structures should be written.
`gc.first` | logical, if TRUE will call gc() first before mode calculation for each structure. This is to avoid memory overload when `ncore > 1`.
`ncore` | number of CPU cores used to do the calculation.
`...` | additional arguments to `aanma`.

### Details

This function builds elastic network model (ENM) using all heavy atoms and performs subsequent normal mode analysis (NMA) on a set of aligned protein structures obtained with function `read.all`. The main purpose is to automate ensemble normal mode analysis using all-atom ENMs.

By default, the effective Hessian for all C-alpha atoms is calculated based on the Hessian built from all heavy atoms (including ligand atoms if `ligand=TRUE`). Returned values include aligned mode vectors and (when `full=TRUE`) a list containing the full ‘nma’ objects one per each structure. When ‘rm.gaps=TRUE’ the unaligned atoms are ommited from output. With default arguments ‘rmsip’ provides RMSIP values for all pairwise structures.

When `outmodes` is provided and is not ‘calpha’ (e.g. ‘noh’. See `aanma` for more details), the function simply returns a list of ‘nma’ objects, one per each structure, and no aligned mode vector is returned. In this case, the arguments `full`, `subspace`, and `rm.gaps` are ignored. This is equivalent to a wrapper function repeatedly calling `aanma`.

### Value

Returns a list of ‘nma’ objects (`outmodes` is provided and is not ‘calpha’) or an ‘enma’ object with the following components:

`fluctuations` | a numeric matrix containing aligned atomic fluctuations with one row per input structure.
`rmsip` | a numeric matrix of pair wise RMSIP values (only the ten lowest frequency modes are included in the calculation).
`U.subspace` | a three-dimensional array with aligned eigenvectors (corresponding to the subspace defined by the first N non-trivial eigenvectors (‘U’) of the ‘nma’ object).
`L` | numeric matrix containing the raw eigenvalues with one row per input structure.
`full.nma` | a list with a `nma` object for each input structure (available only when `full=TRUE`).

### Author(s)

Xin-Qiu Yao & Lars Skjaerven

### See Also

For normal mode analysis on single structure PDB: `aanma`

For conventional C-alpha based normal mode analysis: `nma`, `nma.pdbs`.

For the analysis of the resulting ‘eNMA’ object: `mktrj.enma`, `dccm.enma`, `plot.enma`, `cov.enma`.

Similarity measures: `sip`, `covsoverlap`, `bhattacharyya`, `rmsip`.

Related functionality: `read.all`.

### Examples

      # Needs MUSCLE installed - testing excluded
      if(check.utility("muscle")) {

        ## Fetch PDB files and split to chain A only PDB files
        ids <- c("1a70_A", "1czp_A", "1frd_A", "1fxi_A", "1iue_A", "1pfd_A")
        files <- get.pdb(ids, split = TRUE, path = tempdir())

        ## Sequence Alignement
        aln <- pdbaln(files, outfile = tempfile())

        ## Read all pdb coordinates
        pdbs <- read.all(aln)

        ## Normal mode analysis on aligned data
        modes <- aanma(pdbs, rm.gaps=TRUE)

        ## Plot fluctuation data
        plot(modes, pdbs=pdbs)

        ## Cluster on Fluctuation similariy
        sip <- sip(modes)
        hc <- hclust(dist(sip))
        col <- cutree(hc, k=3)

        ## Plot fluctuation data
        plot(modes, pdbs=pdbs, col=col)

        ## RMSIP is pre-calculated
        heatmap(1-modes$rmsip)

        ## Bhattacharyya coefficient
        bc <- bhattacharyya(modes)
        heatmap(1-bc)

      }

[Package bio3d version 2.3-4 Index]