# 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. The zip file contains two equivalent versions of the package: `veriNA3d_R-3.5.tar.gz` `veriNA3d_R-3.4.tar.gz` The whole package has been developed and tested in R-3.5, which makes it the recommended option. Furthermore, using R-3.5 speeds up the cifParser function, which has a dramatic effect when working with large mmCIF files. The package has been also made available for R-3.4 since some unix users are experiencing problems when installing R-3.5. 3- Unzip the file and copy-paste the desired version of the package in your working directory. 4- Open R and run:   install.packages("veriNA3d_R-3.5.tar.gz", repos = NULL, type="source") 5- If desired, remove the unnecessary .tar.gz files and the .zip file. 6- To start using it, just load the package! library(veriNA3d) ## 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. `queryDescription`: Author description. `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 different RNA groups. `classifyDNA`: Categorizes a structure in different DNA groups.   #### **Input mmCIF data** `cifDownload`: Downloads structure from Protein Data Bank. `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: http://mmcif.wwpdb.org/) `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. `cifAtom_sites` `cifAtom_type` `cifAudit_author` `cifAudit_conform` `cifChem_comp` `cifDatabase_2` `cifEntity` `cifEntry` `cifExptl` `cifPdbx_database_status` `cifStruct` `cifStruct_asym` `cifStruct_keywords`   #### **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 given 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 structure. `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 `findHDR`: Finds High Density Regions in a 2D scatter plot `plot2D`: Scatter plot of angles `plot3Ddens`: 3D view of the density of 2D data. `plotCategorical` `plotCircularDistribution` ## Developers ------------- Diego Gallego Leonardo Darré (Former Developer)     *Molecular Modeling and Bioinformatics Group.* ## License ---------- GPL-3