3\u00a0<\/sup>Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218<\/p>\n\n\n\npKa Data Descriptions<\/h2>\n\n\n\n\u201cProtein Name\u201d and \u201cSpecies\u201d <\/h3>\n\n\n\n
These two columns provide protein names and species for each entry, enabling quick and efficient searches. Users can quickly determine whether a pKa value from the literature is already included in the database by searching for the protein name and species. <\/p>\n\n\n\n
\u201cpKa Classification\u201d <\/h3>\n\n\n\n
The column categorizes each entry as \u201cMain,\u201d \u201cAlt. pKa,\u201d \u201cAlt. pKa (mutant),\u201d or \u201cAlt. pKa (state).\u201d Entries labeled as \u201cMain\u201d represent the most recommended pKa value for a given residue, paired with the most appropriate PDB structure. The label \u201cAlt. pKa\u201d indicates another pKa measurement for the same residue in the same protein as the \u201cMain\u201d entry. \u201cAlt. pKa (mutant)\u201d refers to a pKa measured for the same residue in a mutated version of the protein. \u201cAlt. pKa (state)\u201d denotes a pKa measured in a different state of the protein, such as deoxyhemoglobin versus oxyhemoglobin. For more details on selection of \u201cAlt. pKa (mutant)\u201d and \u201cAlt. pKa (state)\u201d see the description in the \u201cDatabase Curation\u201d section in the paper. <\/p>\n\n\n\n
\u201cAlternative PDBs\u201d<\/h3>\n\n\n\n
The column lists additional PDB structures that are also available for use and similar to the primary PDB structure listed in the “PDB” column. <\/p>\n\n\n\n
“Sequence Identity > 30%” and “Sequence Identity > 90%” <\/h3>\n\n\n\n
These two columns list chains in the format PDB-ID.Chain-ID (e.g., “1EX3.A”) included in this database that have sequence identities greater than 30% and 90%, respectively, compared to the sequence of the current entry’s chain. Sequence identity is calculated using the PairwiseAligner class from the Bio.Align module within the Biopython library. <\/p>\n\n\n\n
\u201cResID in PDB\u201d and \u201cResID in pKa paper\u201d <\/h3>\n\n\n\n
The column “ResID in PDB” lists the residue ID as it appears in the corresponding PDB structure, while “ResID in pKa paper” indicates the residue ID referenced in the original pKa publication when it differs from the PDB. <\/p>\n\n\n\n
\u201cNotes\u201d<\/h3>\n\n\n\n
This column provides, for each residue, details about the selection of the most appropriate pKa value and PDB structure for the “Main” entry, as well as any additional relevant information. <\/p>\n\n\n\n
\u201cWarning\u201d <\/h3>\n\n\n\n
icolumn labels entries under specific conditions: 1) when the pKa is a range or an approximation (labeled as \u201cpKa: range or ~\u201d); 2) when the residue is the C-terminus or N-terminus (labeled as \u201cC\/N-term\u201d); 3) when the residue does not exist in the PDB structure but is present in the protein (labeled as \u201cResID NOT exist\u201d), likely due to its high flexibility and disorder, which makes accurate structural definition difficult; 4) when a mutated structure is used for a wildtype protein, but the mutation is distant from the targeted residue, allowing the structure to be approximately treated as wildtype (labeled as ‘approx. WT’). This column helps users quickly filter out entries that may not meet their needs, such as those unsuitable for direct use in machine learning studies. <\/p>\n","protected":false},"excerpt":{"rendered":"
Understanding pKa values in ionizable protein residues is critical for understanding fundamental protein properties, such as structure, function and interactions. We present a new version of PKAD, named PKAD-R, which is a curated database of experimentally determined protein pKa values. The database builds upon its predecessors, PKAD and PKAD-2, with significant updates and improvements through: […]<\/p>\n","protected":false},"author":302,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-360","page","type-page","status-publish","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/sites.krieger.jhu.edu\/damjanovic-lab\/wp-json\/wp\/v2\/pages\/360","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sites.krieger.jhu.edu\/damjanovic-lab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.krieger.jhu.edu\/damjanovic-lab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.krieger.jhu.edu\/damjanovic-lab\/wp-json\/wp\/v2\/users\/302"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.krieger.jhu.edu\/damjanovic-lab\/wp-json\/wp\/v2\/comments?post=360"}],"version-history":[{"count":5,"href":"https:\/\/sites.krieger.jhu.edu\/damjanovic-lab\/wp-json\/wp\/v2\/pages\/360\/revisions"}],"predecessor-version":[{"id":420,"href":"https:\/\/sites.krieger.jhu.edu\/damjanovic-lab\/wp-json\/wp\/v2\/pages\/360\/revisions\/420"}],"wp:attachment":[{"href":"https:\/\/sites.krieger.jhu.edu\/damjanovic-lab\/wp-json\/wp\/v2\/media?parent=360"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}