pdbmine

A Node.js API for the RCSB Protein Data Bank (PDB)

Installation

npm install pdbmine

If you plan on using pdbmine in your research/project please cite us at https://arxiv.org/abs/1904.03801

Usage

Just require the package.

var miner = require('pdbmine');

You can query the PDB with a string, and a callback function. The result will be an array of PDB ID strings.

miner.query('ribozyme', function(result){
  console.log(result);
});

You can also just get a list of all the PDB IDs:

miner.get_all_ids(function(result){
  console.log(result);
});

You can download a pdb or cif format file of the structure of interest:

miner.download('5k7c', 'pdb', function(data){
  fs = require('fs');
  fs.writeFileSync('5k7c.pdb', data);
});

You can also get info on certain structures by calling the following function. You pass in either a single PDB-ID or a list, a single parameter or a list of parameters, and a callback function.

miner.describe_pdb(['100D','4OJI'], ['depositionDate', 'macromoleculeType'], function(result){
  console.log(result);
});

Valid parameters can be accessed via miner.fields. They are also listed at the bottom of this README

You can filter the results from describe_pdb() using the standard Array filtering method:

miner.describe_pdb(['100D','4OJI'], ['depositionDate', 'macromoleculeType'], function(result){
  filtered_result = result.filter(obj => obj.macromoleculeType == 'Protein');
  console.log(filtered_result);
});

Don't like callback functions? You can avoid passing in callback functions and instead use Promises as follows:

miner.query('ribozyme')
     .then(results => miner.describe_pdb(results, ['macromoleculeType']))
     .then(descriptions => descriptions.filter(obj => obj.macromoleculeType == 'RNA'))
     .then(rnas => {
     	console.log(rnas);
     });

Parameters

Report Name	Field Name
Structure Summary Report (StructureSummary)	atomSiteCount
	authors
	classification
	depositionDate
	experimentalTechnique
	macromoleculeType
	ndbId
	pdbDoi
	releaseDate
	residueCount
	resolution
	revisionDate
	structureMolecularWeight
	structureTitle
Sequence Report (Sequence)	chainLength
	db_code
	db_name
	entityId
	entityMacromoleculeType
	kabschSander
	molecularWeight
	sequence
Ligand Report (Ligands)	InChI
	InChIKey
	ligandFormula
	ligandId
	ligandImage
	ligandMolecularWeight
	ligandName
	ligandSmiles
Binding Affinity Report (BindingAffinity)	EC50
	IC50
	Ka
	Kd
	Ki
	deltaG
	deltaH
	deltaS
	hetId
Biological Detail Report (BiologicalDetails)	biologicalProcess
	cellularComponent
	compound
	ecNo
	expressionHost
	molecularFunction
	plasmid
	source
	taxonomyId
Cluster Entity Report (ClusterEntity)	authorAssignedEntityName
	clusterNumber100
	clusterNumber30
	clusterNumber40
	clusterNumber50
	clusterNumber70
	clusterNumber90
	clusterNumber95
	entityId
	geneName
	idNum
	rankNumber100
	rankNumber30
	rankNumber40
	rankNumber50
	rankNumber70
	rankNumber90
	rankNumber95
	synonym
	taxonomy
	taxonomyId
	uniprotAcc
	uniprotAlternativeNames
	uniprotRecommendedName
Domains Report (Domains)	cathDescription
	cathId
	pfamAccession
	pfamDescription
	pfamId
	scopDomain
	scopFold
	scopId
Crystallization Report (Crystallization)	crystallizationMethod
	crystallizationTempK
	densityMatthews
	densityPercentSol
	pdbxDetails
	phValue
Unit Cell Dimension Report (UnitCellDimensions)	Z_PDB
	lengthOfUnitCellLatticeA
	lengthOfUnitCellLatticeB
	lengthOfUnitCellLatticeC
	spaceGroup
	unitCellAngleAlpha
	unitCellAngleBeta
	unitCellAngleGamma
Data Collection Detail Report (DataCollectionDetails)	collectionDate
	collectionTemperature
	device
	diffractionSource
	diffrnId
Refinement Detail Report (RefinementDetails)	averageBFactor
	rAll
	rFree
	rObserved
	rWork
	refinementResolution
Refinement Parameter Report (refinementParameters)	highResolutionLimit
	reflectionsForRefinement
	structureDeterminationMethod
Software Report (NmrSoftware)	authors
	name
	version
NMR Spectrometer Report (NmrSpectrometer)	fieldStrength
	manufacturer
	model
nmrExperimentalSampleConditions Report (NMRExperimentalSampleConditions)	contents
	ionicStrength
	ph
	pressure
	pressureUnits
	solventSystem
	temperature
	type
NMR Representative Report (NmrRepresentative)	conformerId
	selectionCriteria
NMR Refine Report (NMRRefinement)	details
	method
NMR Ensemble Report (NmrEnsemble)	conformerSelectionCriteria
	totalConformersCalculated
	totalConformersSubmitted
EM Structure Report (EMStructure)	emResolution
	emDiffractionResolution
	reconstructionMethod
	symmetryType
	pointSymmetry
	aggregationState
	embedding
	staining
	vitrification
	emdbMap
	additionalMap
Citation Report (Citation)	abstractTextShort
	authors
	doi
	firstPage
	journalName
	lastPage
	meshTerms
	pmc
	publicationYear
	pubmedId
	title
	volumeId
Other Citation Report (OtherCitations)	authors
	firstPage
	journalName
	pmc
	publicationYear
	pubmedId
	title
	volumeId
Structural Genomics Centers Report (SGProject)	centerInitial
	centerName
	projectName