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veriNA3d package
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# R PACKAGE: veriNA3d
VeriNA3d is an R package for the analysis of Nucleic Acid structural data. The software was developed on top of bio3d (Grant et al, 2006) with a higher level of abstraction. In addition of single-structure analyses, veriNA3d also implements pipelines to handle whole datasets of mmCIF/PDB structures. As far as we know, no similar software has been previously distributed, thus it aims to fill a gap in the data mining pipelines of PDB structural data analyses.
## Installation
Instructions for Unix systems
1- Make sure you have all the dependencies already installed in R. If not the case, open R and run:
install.packages(c("bio3d", "circlize", "jsonlite", "plot3D", "MASS", "RColorBrewer", "RANN"))
2- Download veriNA3d from GitLab. It will download a compressed .zip file with two versions of the package:
A- veriNA3d_R-3.5.tar.gz
B- veriNA3d_R-3.4.tar.gz
Option A is the recommended one, since it dramatically speeds up the cifParser function. However, Option B offers the package for R >= 3.4, since R-3.5 might be difficult to install for some unix users.
3- Open R and run:
install.packages(veriNA3d_R-3.5.tar.gz, repos = NULL, type="source")
## Documentation
### Dataset level
`getLeontisList`: Get list of representative/non-redundant RNA structures organized in Equivalence Classes (source: Leontis & Zirbel, 2012)
`getAltRepres`: Apply filters (e.g. just protein-RNA structures) to select other representants from the members of each class
`represAsDataFrame`: From the output of getLeontisList or getAltRepres, generate a data.frame in which each row corresponds to a RNA chain, rather than an Equivalence Class
`pipeNucData`: From a list of RNA structures/chains computes and returns structural data at the level of the nucleotide
`pipeProtNucData`: From a list of protein-RNA structures computes and returns the interaction sites distances and atoms
`applyToPDB`: Applies a desired function to a list of PDB IDs
`queryEntryList`: Returns the whole list of PDB IDs in the database
`queryObsoleteList`: Returns the list of Obsolete PDB IDs in the database
`cleanByPucker`: From the output of pipeNucData subsets a desired subset of nucleotides in a given puckering conformation
### Single-structure level
#### **Functions to query PDB data using the PDBe (EMBL-EBI) REST API or a mirror API from the MMB Lab** (All of them take a PDB ID as input)
`queryAuthors`: List of authors
`queryReldate`: Release date
`queryDepdate`: Deposition date
`queryRevdate`: Revision date
`queryCompound`: PDB structure title
`queryCompType`: Compound type (e.g. Nuc or Prot-nuc)
`queryChains`: Chain information
`queryEntities`: Entitity information
`countEntities`: In a given pdbID it counts the total number of each different kind of entity (RNA, DNA, Protein ...)
`queryFormats`: File formats for the given ID
`queryHeader`: PDB Header
`queryHetAtms`: HETATM entities in structure (includes modified residues, ions and ligands)
`hasHetAtm`: Checks wether a a given structure contains a particular HETATM entity. It makes use of queryHetAtms
`queryModres`: Modified residues
`queryLigands`: Ligands in structure
`queryOrgLigands`: Ligands in structure (substracting ions)
`queryResol`: Resolution (if applicable)
`queryTechnique`: Experimental Technique
`queryStatus`: Released/Obsolete and related status information
`queryNDBId`: Cross-reference NDB ID
`queryAPI`: Subfunction of all the previous, which can be used to make alternative queries
#### **Classify PDB structures** (PDB ID as input)
`classifyRNA`: Categorizes a structure in "nakedRNA", "protRNA", "ligandRNA", "DNARNA" or "NoRNA"
`classifyDNA`: Categorizes a structure in "nakedDNA", "protDNA", "ligandDNA", "DNARNA" or "NoDNA"
#### **Input mmCIF data**
`cifParser`: Reads the 14th common sections of all mmCIF files in the PDB and generates a CIF S4 object.
`cifAsPDB`: Wrapper of cifParser that generates a pdb object (bio3d compatible S3 object).
#### **CIF accessors** (Find descriptions in mmCIF dicctionary:
`cifAtom_site`: Access the coordinates of a CIF object (read by cifParser). The resulting object is not compatible with bio3d functions, see cifAsPDB for that.
#### **Structure analysis**
`selectModel`: Selects the model of interest
`findBindingSite`: Same as pipeProtNucData for a single structure
`measureEntityDist`: Measures distances between given entities
`measureElenoDist`: Measures distances between gicen atoms
`trimSphere`: Trim a pdb object and a surrounding sphere of atoms
`trimByID`: Same as trimSphere using the IDs and output of pipeNucData
`checkNuc`: Checks the integrity of all the nucleotides in a given Nucleic Acid structure
`measureNuc`: Measures a defult/desired set of distances, angles and torsional angles for a given Nucleic Acid strucutre
`rVector`: Computes the rVectors between all nucleobases of a structure (source: Bottaro et al, 2014)
`eRMSD`: Compares structures with the same number of residues using the rVectors (source: Bottaro et al, 2014)
`dssr`: Wrapper of DSSR software (source: Lu et al, 2015), if installed.
### Exploratory analysis
## Developers
Diego Gallego
Leonardo Darré (Former Developer)
*Molecular Modeling and Bioinformatics Group.*
## License
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