diff --git a/src/extensions/anvil/algorithm.ts b/src/extensions/anvil/algorithm.ts index 30b582e32183905649c5613a721e49be9fd929ad..165079ad9ed2156f6a9d7570b0fd513577e7e8b4 100644 --- a/src/extensions/anvil/algorithm.ts +++ b/src/extensions/anvil/algorithm.ts @@ -44,17 +44,29 @@ export const ANVILParams = { minThickness: PD.Numeric(20, { min: 10, max: 30, step: 1}, { description: 'Minimum membrane thickness used during refinement' }), maxThickness: PD.Numeric(40, { min: 30, max: 50, step: 1}, { description: 'Maximum membrane thickness used during refinement' }), asaCutoff: PD.Numeric(40, { min: 10, max: 100, step: 1 }, { description: 'Relative ASA cutoff above which residues will be considered' }), - adjust: PD.Numeric(14, { min: 0, max: 30, step: 1 }, { description: 'Minimum length of membrane-spanning regions (original values: 14 for alpha-helices and 5 for beta sheets). Set to 0 to not optimize membrane thickness.' }) + adjust: PD.Numeric(14, { min: 0, max: 30, step: 1 }, { description: 'Minimum length of membrane-spanning regions (original values: 14 for alpha-helices and 5 for beta sheets). Set to 0 to not optimize membrane thickness.' }), + tmdetDefinition: PD.Boolean(false, { description: `Use TMDET's classification of membrane-favoring amino acids. TMDET's classification shows better performance on porins and other beta-barrel structures.` }) }; export type ANVILParams = typeof ANVILParams export type ANVILProps = PD.Values<ANVILParams> +/** ANVIL-specific (not general) definition of membrane-favoring amino acids */ +const ANVIL_DEFINITION = new Set(['ALA', 'CYS', 'GLY', 'HIS', 'ILE', 'LEU', 'MET', 'PHE', 'SER', 'TRP', 'VAL']); +/** TMDET-specific (not general) definition of membrane-favoring amino acids */ +const TMDET_DEFINITION = new Set(['LEU', 'ILE', 'VAL', 'PHE', 'MET', 'GLY', 'TRP', 'TYR']); + /** * Implements: * Membrane positioning for high- and low-resolution protein structures through a binary classification approach * Guillaume Postic, Yassine Ghouzam, Vincent Guiraud, and Jean-Christophe Gelly * Protein Engineering, Design & Selection, 2015, 1–5 * doi: 10.1093/protein/gzv063 + * + * ANVIL is derived from TMDET, the corresponding classification of hydrophobic amino acids is provided as optional parameter: + * Gabor E. Tusnady, Zsuzsanna Dosztanyi and Istvan Simon + * Transmembrane proteins in the Protein Data Bank: identification and classification + * Bioinformatics, 2004, 2964-2972 + * doi: 10.1093/bioinformatics/bth340 */ export function computeANVIL(structure: Structure, props: ANVILProps) { return Task.create('Compute Membrane Orientation', async runtime => { @@ -87,6 +99,7 @@ async function initialize(structure: Structure, props: ANVILProps, accessibleSur const offsets = new Array<number>(); const exposed = new Array<number>(); const hydrophobic = new Array<boolean>(); + const definition = props.tmdetDefinition ? TMDET_DEFINITION : ANVIL_DEFINITION; const vec = v3zero(); for (let i = 0, il = structure.units.length; i < il; ++i) { @@ -121,7 +134,7 @@ async function initialize(structure: Structure, props: ANVILProps, accessibleSur offsets.push(structure.serialMapping.getSerialIndex(l.unit, l.element)); if (AccessibleSurfaceArea.getValue(l, accessibleSurfaceArea) / MaxAsa[label_comp_id(l)] > asaCutoff) { exposed.push(structure.serialMapping.getSerialIndex(l.unit, l.element)); - hydrophobic.push(isHydrophobic(label_comp_id(l))); + hydrophobic.push(isHydrophobic(definition, label_comp_id(l))); } } } @@ -566,11 +579,9 @@ namespace HphobHphil { } } -/** ANVIL-specific (not general) definition of membrane-favoring amino acids */ -const HYDROPHOBIC_AMINO_ACIDS = new Set(['ALA', 'CYS', 'GLY', 'HIS', 'ILE', 'LEU', 'MET', 'PHE', 'SER', 'TRP', 'VAL']); -/** Returns true if ANVIL considers this as amino acid that favors being embedded in a membrane */ -export function isHydrophobic(label_comp_id: string): boolean { - return HYDROPHOBIC_AMINO_ACIDS.has(label_comp_id); +/** Returns true if the definition considers this as membrane-favoring amino acid */ +export function isHydrophobic(definition: Set<string>, label_comp_id: string): boolean { + return definition.has(label_comp_id); } /** Accessible surface area used for normalization. ANVIL uses 'Total-Side REL' values from NACCESS, from: Hubbard, S. J., & Thornton, J. M. (1993). naccess. Computer Program, Department of Biochemistry and Molecular Biology, University College London, 2(1). */