BUILT-IN MATHEMATICA SYMBOL
ProteinData
ProteinData["prot"]
gives the reference amino acid sequence for the protein prot.
ProteinData["prot", "property"]
gives the value of the specified property for the protein prot.
- Proteins are specified by standard names such as
.
- ProteinData[] gives a list of all reference human proteins.
- Protein sequences are represented as strings of standard single-letter amino acid codes.
- Fundamental properties include:
-
| "MolecularWeight" | total molecular weight in daltons |
- Sequence properties for proteins include:
-
| "DNACodingSequence" | base pair sequence coding for the protein |
| "DNACodingSequenceLength" | length of base pair sequence coding for the protein |
| "Gene" | gene that codes for the protein |
| "Sequence" | amino acid sequence for the protein |
| "SequenceLength" | length of amino acid sequence for the protein |
- Protein structures may contain additional elements not explicitly encoded in the original DNA sequence.
- Molecular structure properties based on residues include:
-
| "DihedralAngles" | list of dihedral angles  ,  ,  in radians |
| "SecondaryStructureRules" | list of rules giving start and end positions of helix, sheet, etc. structures |
- Molecular structure properties based on individual atoms include:
-
| "AdditionalAtomPositions" | list of 3D coordinates of additional atoms |
| "AdditionalAtomTypes" | list of element symbols for additional atoms |
| "AtomPositions" | list of 3D coordinates of protein atoms |
| "AtomRoles" | list of structural roles for protein atoms |
| "AtomTypes" | list of element symbols for protein atoms |
| "GyrationRadius" | radius of gyration |
| "MoleculePlot" | 3D molecular structure plot |
- Distances are measured in picometers.
- ProteinData["prot", "prop", grouping] gives molecular structure properties with various groupings:
-
| {} | no grouping |
| "Chain" | group by chain |
| "Residue" | group by residue |
| {g1,g2,...} | list of grouping criteria |
- Properties associated with chains within structures include:
-
| "ChainLabels" | list of identifiers for 3D structure chains |
| "ChainSequences" | list of amino acid sequences for 3D structure chains |
- Protein common domain properties include:
-
| "DomainIDs" | NCBI CDD numbers of domains |
| "DomainPositions" | positions of domains in the protein sequence |
| "Domains" | names of domains in the protein |
- Functional properties include:
-
| "BiologicalProcesses" | biological processes associated with the protein |
| "CellularComponents" | cellular components in which the protein is found |
| "MolecularFunctions" | molecular functions of the protein |
- Protein identification properties include:
-
| "AlternateNames" | alternate traditional names |
| "GeneID" | GeneID number string for the protein's gene |
| "Name" | traditional name |
| "NCBIAccessions" | NCBI accession strings |
| "PDBIDList" | list of all PDB ID strings |
| "PrimaryPDBID" | PDB ID chosen in Mathematica for structure properties, etc. |
| "StandardName" | standard Mathematica name |
- ProteinData["prot", "prop", "Units"] gives the units for a particular property value.
Get a list of human proteins:
Out[1]//Short= |
| |  |
| Out[2]= |  |
Display the ribbon diagram:
| Out[1]= |  |
Get the amino acid sequence of a protein:
| Out[1]= |  |
Get the molecular weight of a protein:
| Out[1]= |  |
Get the number of amino acids in a protein sequence:
| Out[1]= |  |
Get the coordinates of atoms in a 3D protein structure:
Out[1]//Short= |
| |  |
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