{"id":15,"date":"2021-11-30T13:14:22","date_gmt":"2021-11-30T13:14:22","guid":{"rendered":"https:\/\/www.ebi.ac.uk\/research-beta\/thornton\/home\/"},"modified":"2024-05-23T15:52:16","modified_gmt":"2024-05-23T15:52:16","slug":"home","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/research\/thornton\/","title":{"rendered":"Home"},"content":{"rendered":"\n\n\n\n\n<div >\n\n    \n    \n<\/div>\n\n\n\n\n<div class=\"vf-grid | vf-grid__col-3\"><div class=\"vf-grid__col--span-2\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<p class=\"wp-block-paragraph\"><em>Please note: the Thornton Group is no longer able to take on new students, trainees or post-doctoral fellows. <\/em><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">We explore the structure, function and evolution of proteins. These basic studies facilitate our ability to understand how proteins work and to interpret coding variations in humans and their impact on healthy ageing and disease. Our research is focused in three distinct but related areas:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>We seek to understand how enzymes work and how they evolve to perform new enzyme functions, based on structural data. We have shown that most enzyme functions have evolved from other functions; this opens the path to rational design of novel enzymes with new functions and mechanisms. We also develop computational tools based on our analyses, to improve enzyme design. Our analysis of enzyme active sites reveals a high degree of structural conservation of the catalytic residues (shown by the grey outlines). This allows us to derive representative structural templates (black outlines, derived from PDB entry 1n4o) for each enzyme type. These can be used to search for related enzymes or pseudo-enzymes.<\/li>\n\n\n\n<li>Our study of human coding variations aims to use protein structural knowledge to interpret their effects. Using the CATH domain database, we study variations occurring in related domains and explore how their genomic context influences the resultant phenotype.<\/li>\n\n\n\n<li>Our work on enzymes and variants is ultimately related to human health, ageing and disease. Our goal is to trace the steps from the molecular protein variant or ligand and its effect on the protein\u2019s function and, from there, to the organismal \u2018disease and ageing\u2019 sub-phenotype. In our ageing studies, we aim to combine data over multiple organisms and multiple data types to define sub-phenotypes of ageing to improve our understanding of the molecular basis of ageing. We will explore why ageing makes us more susceptible to some diseases and use computational methods to identify small molecules that may have an impact on ageing.<\/li>\n<\/ul>\n\n\n\n<figure class=\"vf-figure wp-block-image size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"490\" height=\"442\" class=\"vf-figure__image\" src=\"https:\/\/www.ebi.ac.uk\/research-beta\/thornton\/wp-content\/uploads\/2022\/01\/image-2.png\" alt=\"\" class=\"wp-image-188\" srcset=\"https:\/\/www.ebi.ac.uk\/research\/thornton\/wp-content\/uploads\/2022\/01\/image-2.png 490w, https:\/\/www.ebi.ac.uk\/research\/thornton\/wp-content\/uploads\/2022\/01\/image-2-300x271.png 300w\" sizes=\"auto, (max-width: 490px) 100vw, 490px\" \/><figcaption class=\"vf-figure__caption\">Catalytic Templates for Class A Beta-lactamases. This shows a superposition of the active site residues taken from 244 related but \u2018unique\u2019 structures. Most residues superpose well, but the Ser\/Thr residues (which occur in different members of the family) can be seen to adopt two alternative conformations in these structures.<\/figcaption><\/figure>\n\n\n\n<h2 class=\"wp-block-heading\">Future projects<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">For our enzyme work, our central question is whether we can predict the evolution of enzyme function \u2013 both in terms of adapting to operate on new substrates and evolving new mechanisms. Can we relate changes in function to changes in the structure of the enzyme and changes in the environment? Can we automatically predict or validate enzyme catalytic mechanisms <em>in silico<\/em> from structural data? We will further develop our data resources (M-CSA) and websites (PDBsum) and develop novel methods to predict transformations and mechanisms using knowledge-based and deep-learning approaches.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">For coding variants, we will enhance our web tool (VarSite) to relate variant, 3D structure and function to help non-experts understand the impact of coding variants and how they generate disease phenotypes. &nbsp;To address these questions, we plan to:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>develop new methods to analyse the effects of mutations in ligand binding sites<\/li>\n\n\n\n<li>explore variants in co-factor binding sites and their impact on function<\/li>\n\n\n\n<li>apply our methods to specific genes of interest in collaboration with \u2018domain\u2019 experts<\/li>\n\n\n\n<li>explore how the same mutations can cause many diseases, and how one disease can have many causes.<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\">For ageing, we will develop tools to combine transcriptome data sets and analyse a small number of common diseases and the impact of ageing on their occurrence.<\/p>\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<h2 class=\"wp-block-heading\">Selected publications<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Laskowski RA, Stephenson JD<\/strong>, Sillitoe I, Orengo CA, <strong>Thornton JM<\/strong>. <a href=\"https:\/\/doi.org\/10.1002\/pro.3746\">VarSite: Disease variants and protein structure (2020)<\/a>. <em>Protein Science<\/em> 29, 111-119<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Ribeiro AJ, Tyzack JD, Borkakoti N, Thornton JM<\/strong>. <a href=\"https:\/\/doi.org\/10.1111\/febs.15142\">Identifying pseudoenzymes using functional annotation: pitfalls of common practice (2020)<\/a>. <em>The FEBS Journal<\/em> 287, 4128-4140<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>D\u00f6nerta\u015f HM, Fabian DK<\/strong>, Fuentealba Valenzuela MF, Partridge L, <strong>Thornton JM<\/strong>. <a href=\"https:\/\/doi.org\/10.1038\/s43587-021-00051-5\">Common genetic associations between age-related diseases (2020)<\/a>. Nature Ageing ref.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Laskowski, RA, Thornton, JM.<\/strong> <a href=\"https:\/\/doi.org\/10.1002\/pro.4238\">PDBsum extras: SARS-CoV-2 and AlphaFold models (2022)<\/a>. <em>Protein Science<\/em> 31: 283-289.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Thornton J M, Laskowski R A, Borkakoti N<\/strong>. <a href=\"https:\/\/doi.org\/10.1038\/s41591-021-01533-0\">AlphaFold heralds a data-driven revolution in biology and medicine (2021)<\/a>. <em>Nat Med<\/em>, <strong>27<\/strong>, 1666\u20131669.<\/p>\n\n<\/div>\n<\/div>\n<\/div>\n\n\n<div class=\"embl-grid embl-grid--has-centered-content | vf-u-margin__top--800\">\n    <div class=\"vf-section-header\">\n  <h2 class=\"vf-section-header__heading\">\n    <a class=\"vf-section-header__heading vf-section-header__heading--is-link\" href=\"https:\/\/www.ebi.ac.uk\/services\"\n      id=\"section-link\"> Data resources <svg aria-hidden=\"true\"\n        class=\"vf-section-header__icon | vf-icon vf-icon-arrow--inline-end\" width=\"24\" height=\"24\"\n        xmlns=\"http:\/\/www.w3.org\/2000\/svg\">\n        <path\n          d=\"M0 12c0 6.627 5.373 12 12 12s12-5.373 12-12S18.627 0 12 0C5.376.008.008 5.376 0 12zm13.707-5.209l4.5 4.5a1 1 0 010 1.414l-4.5 4.5a1 1 0 01-1.414-1.414l2.366-2.367a.25.25 0 00-.177-.424H6a1 1 0 010-2h8.482a.25.25 0 00.177-.427l-2.366-2.368a1 1 0 011.414-1.414z\"\n          fill=\"\" fill-rule=\"nonzero\"><\/path>\n      <\/svg><\/a><\/h2><\/div>\n    <div>\n    <div class=\"vf-content-hub-html\" data-cache=\"9c7122bd\">\n  <!-- Generated by: http:\/\/content.embl.org\/api\/v1\/pattern.html?filter-content-type=data_resource&amp;filter-field-contains%5Bfield_resource_primary_team.entity.title%5D=Thornton%20Group&amp;limit=30&amp;pattern=vf-summary-image&amp;sort-field-value%5Btitle%5D=ASC -->\n            <article class=\"vf-summary vf-summary--has-image vf-summary-image\">\n                                \n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/Tools\/archschema\/\">\n            <img decoding=\"async\" class=\"vf-summary__image vf-summary__image--thumbnail\" src=\"https:\/\/content.embl.org\/sites\/default\/files\/styles\/medium\/public\/03-2025\/EMBL_EBI-logo.png?itok=1Ym2qeKf\" alt=\"ArchSchema\">\n          <\/a>\n        \n                          <h3 class=\"vf-summary__title\">\n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/Tools\/archschema\/\">ArchSchema<\/a>\n                      <\/h3>\n        \n                                          <p class=\"vf-summary__text\">\n            ArchSchema is a java webstart application that generates dynamic plots of related Pfam domain architectures. The protein sequences having each architecture can be displayed on the plot and separately listed. Where there is 3D structural information in the PDB, the relevant PDB codes can be shown on \u2026\n          <\/p>\n              <\/article>\n          <article class=\"vf-summary vf-summary--has-image vf-summary-image\">\n                                \n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/sidechains\/\">\n            <img decoding=\"async\" class=\"vf-summary__image vf-summary__image--thumbnail\" src=\"https:\/\/content.embl.org\/sites\/default\/files\/styles\/medium\/public\/06-2026\/database-tool-icon_0-2-1.png?itok=ERcHjrr1\" alt=\"Atlas of Protein Side-Chain Interactions\">\n          <\/a>\n        \n                          <h3 class=\"vf-summary__title\">\n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/sidechains\/\">Atlas of Protein Side-Chain Interactions<\/a>\n                      <\/h3>\n        \n                                          <p class=\"vf-summary__text\">\n            This atlas depicts how amino acid side-chains pack against one anotherwithin the knownprotein structures. This packing, which is governed by the interactions between the 20 different types of side-chains, determines the structure, function, and stability of proteins.\n          <\/p>\n              <\/article>\n          <article class=\"vf-summary vf-summary--has-image vf-summary-image\">\n                                \n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/CSA\">\n            <img decoding=\"async\" class=\"vf-summary__image vf-summary__image--thumbnail\" src=\"https:\/\/content.embl.org\/sites\/default\/files\/styles\/medium\/public\/06-2026\/logo2a-1-1.png?itok=aawgw7TP\" alt=\"Catalytic Site Atlas\">\n          <\/a>\n        \n                          <h3 class=\"vf-summary__title\">\n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/CSA\">Catalytic Site Atlas<\/a>\n                      <\/h3>\n        \n                                          <p class=\"vf-summary__text\">\n            CSA is a resource of catalytic sites and residues that have been identified in enzymes using structural data.\n          <\/p>\n              <\/article>\n          <article class=\"vf-summary vf-summary--has-image vf-summary-image\">\n                                \n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/CoFactor\/\">\n            <img decoding=\"async\" class=\"vf-summary__image vf-summary__image--thumbnail\" src=\"https:\/\/content.embl.org\/sites\/default\/files\/styles\/medium\/public\/03-2025\/EMBL_EBI-logo.png?itok=1Ym2qeKf\" alt=\"Cofactor database\">\n          <\/a>\n        \n                          <h3 class=\"vf-summary__title\">\n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/CoFactor\/\">Cofactor database<\/a>\n                      <\/h3>\n        \n                                          <p class=\"vf-summary__text\">\n            Organic enzyme cofactors are involved in many enzyme reactions. Therefore, the analysis of cofactors is crucial to gain a better understanding of enzyme catalysis. To aid this, we have created the CoFactor database. It provides a web interface to access hand-curated data extracted from the literatur\u2026\n          <\/p>\n              <\/article>\n          <article class=\"vf-summary vf-summary--has-image vf-summary-image\">\n                                \n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/CSS_NEW\">\n            <img decoding=\"async\" class=\"vf-summary__image vf-summary__image--thumbnail\" src=\"https:\/\/content.embl.org\/sites\/default\/files\/styles\/medium\/public\/03-2025\/database-tool-icon_0-2-1.png?itok=q8BfADlO\" alt=\"CSS\">\n          <\/a>\n        \n                          <h3 class=\"vf-summary__title\">\n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/CSS_NEW\">CSS<\/a>\n                      <\/h3>\n        \n                                          <p class=\"vf-summary__text\">\n            \nSearches a protein structure for likely catalytic sites\n          <\/p>\n              <\/article>\n          <article class=\"vf-summary vf-summary--has-image vf-summary-image\">\n                                \n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/enzymes\/\">\n            <img decoding=\"async\" class=\"vf-summary__image vf-summary__image--thumbnail\" src=\"https:\/\/content.embl.org\/sites\/default\/files\/styles\/medium\/public\/03-2025\/EMBL_EBI-logo.png?itok=1Ym2qeKf\" alt=\"EC-PDB\">\n          <\/a>\n        \n                          <h3 class=\"vf-summary__title\">\n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/enzymes\/\">EC-PDB<\/a>\n                      <\/h3>\n        \n                                          <p class=\"vf-summary__text\">\n            This database contains the known enzyme structures that have been deposited in the Protein Data Bank (PDB).\n          <\/p>\n              <\/article>\n          <article class=\"vf-summary vf-summary--has-image vf-summary-image\">\n                                \n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/FunTree\/\">\n            <img decoding=\"async\" class=\"vf-summary__image vf-summary__image--thumbnail\" src=\"https:\/\/content.embl.org\/sites\/default\/files\/styles\/medium\/public\/03-2025\/funtree-logo-1-1.png?itok=FH7crcIn\" alt=\"FunTree\">\n          <\/a>\n        \n                          <h3 class=\"vf-summary__title\">\n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/FunTree\/\">FunTree<\/a>\n                      <\/h3>\n        \n                                          <p class=\"vf-summary__text\">\n            FunTree provides a range of data resources to detect the evolution of enzyme function within distant structurally related clusters within domain super families as determined by CATH . To access the resource enter a specific CATH superfamily code or search for a structure \/ sequence \/ function (eithe\u2026\n          <\/p>\n              <\/article>\n          <article class=\"vf-summary vf-summary--has-image vf-summary-image\">\n                                \n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/LigSearch\">\n            <img decoding=\"async\" class=\"vf-summary__image vf-summary__image--thumbnail\" src=\"https:\/\/content.embl.org\/sites\/default\/files\/styles\/medium\/public\/03-2025\/database-tool-icon_0-2-1.png?itok=q8BfADlO\" alt=\"LigSearch\">\n          <\/a>\n        \n                          <h3 class=\"vf-summary__title\">\n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/LigSearch\">LigSearch<\/a>\n                      <\/h3>\n        \n                                          <p class=\"vf-summary__text\">\n            Identifies small molecules likely to bind to given protein\n          <\/p>\n              <\/article>\n          <article class=\"vf-summary vf-summary--has-image vf-summary-image\">\n                                \n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/MACiE\/\">\n            <img decoding=\"async\" class=\"vf-summary__image vf-summary__image--thumbnail\" src=\"https:\/\/content.embl.org\/sites\/default\/files\/styles\/medium\/public\/06-2026\/database-tool-icon_0-2-1.png?itok=ERcHjrr1\" alt=\"MACiE\">\n          <\/a>\n        \n                          <h3 class=\"vf-summary__title\">\n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/MACiE\/\">MACiE<\/a>\n                      <\/h3>\n        \n                                          <p class=\"vf-summary__text\">\n            Mechanism, Annotation and Classification in Enzymes. Query for an enzyme, and return enzyme mechanism.\n          <\/p>\n              <\/article>\n          <article class=\"vf-summary vf-summary--has-image vf-summary-image\">\n                                \n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/pdbsum\">\n            <img decoding=\"async\" class=\"vf-summary__image vf-summary__image--thumbnail\" src=\"https:\/\/content.embl.org\/sites\/default\/files\/styles\/medium\/public\/06-2026\/pdbsum_logo-2-1.gif?itok=P54pbIfE\" alt=\"PDBsum\">\n          <\/a>\n        \n                          <h3 class=\"vf-summary__title\">\n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/pdbsum\">PDBsum<\/a>\n                      <\/h3>\n        \n                                          <p class=\"vf-summary__text\">\n            This pictorial database provides an overview of macromolecular structures deposited in the Protein Data Bank archive.\n          <\/p>\n              <\/article>\n          <article class=\"vf-summary vf-summary--has-image vf-summary-image\">\n                                \n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/pdbsum\/Generate.html\">\n            <img decoding=\"async\" class=\"vf-summary__image vf-summary__image--thumbnail\" src=\"https:\/\/content.embl.org\/sites\/default\/files\/styles\/medium\/public\/06-2026\/database-tool-icon_0-2-1.png?itok=ERcHjrr1\" alt=\"PDBsum Generate\">\n          <\/a>\n        \n                          <h3 class=\"vf-summary__title\">\n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/pdbsum\/Generate.html\">PDBsum Generate<\/a>\n                      <\/h3>\n        \n                                          <p class=\"vf-summary__text\">\n            Protein structure analyses, inlcuding secondary structure determination, quality assessment, protein -ligand -protein -DNA interactions.\n          <\/p>\n              <\/article>\n          <article class=\"vf-summary vf-summary--has-image vf-summary-image\">\n                                \n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/pita\/\">\n            <img decoding=\"async\" class=\"vf-summary__image vf-summary__image--thumbnail\" src=\"https:\/\/content.embl.org\/sites\/default\/files\/styles\/medium\/public\/03-2025\/database-tool-icon_0-2-1.png?itok=q8BfADlO\" alt=\"PITA\">\n          <\/a>\n        \n                          <h3 class=\"vf-summary__title\">\n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/pita\/\">PITA<\/a>\n                      <\/h3>\n        \n                                          <p class=\"vf-summary__text\">\n            \nSuggests most likely biological unit for X-ray structure of protein\n          <\/p>\n              <\/article>\n          <article class=\"vf-summary vf-summary--has-image vf-summary-image\">\n                                \n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/software\/PoreLogo\/\">\n            <img decoding=\"async\" class=\"vf-summary__image vf-summary__image--thumbnail\" src=\"https:\/\/content.embl.org\/sites\/default\/files\/styles\/medium\/public\/11-2025\/logo_porelogo_small-1.jpg?itok=jaT3v0S7\" alt=\"PoreLogo\">\n          <\/a>\n        \n                          <h3 class=\"vf-summary__title\">\n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/software\/PoreLogo\/\">PoreLogo<\/a>\n                      <\/h3>\n        \n                                          <p class=\"vf-summary__text\">\n            Generates logo showing conservation of pore-lining residues in transmembrane protein structures\n          <\/p>\n              <\/article>\n          <article class=\"vf-summary vf-summary--has-image vf-summary-image\">\n                                \n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/software\/PoreWalker\/\">\n            <img decoding=\"async\" class=\"vf-summary__image vf-summary__image--thumbnail\" src=\"https:\/\/content.embl.org\/sites\/default\/files\/styles\/medium\/public\/06-2026\/database-tool-icon_0-2-1.png?itok=ERcHjrr1\" alt=\"PoreWalker\">\n          <\/a>\n        \n                          <h3 class=\"vf-summary__title\">\n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/software\/PoreWalker\/\">PoreWalker<\/a>\n                      <\/h3>\n        \n                                          <p class=\"vf-summary__text\">\n            Detects and characterises transmembrane protein channels from their 3D structure\n          <\/p>\n              <\/article>\n          <article class=\"vf-summary vf-summary--has-image vf-summary-image\">\n                                \n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/profunc\">\n            <img decoding=\"async\" class=\"vf-summary__image vf-summary__image--thumbnail\" src=\"https:\/\/content.embl.org\/sites\/default\/files\/styles\/medium\/public\/06-2026\/database-tool-icon_0-2-1.png?itok=ERcHjrr1\" alt=\"ProFunc\">\n          <\/a>\n        \n                          <h3 class=\"vf-summary__title\">\n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/profunc\">ProFunc<\/a>\n                      <\/h3>\n        \n                                          <p class=\"vf-summary__text\">\n            Protein function prediction\n          <\/p>\n              <\/article>\n          <article class=\"vf-summary vf-summary--has-image vf-summary-image\">\n                                \n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/sas\">\n            <img decoding=\"async\" class=\"vf-summary__image vf-summary__image--thumbnail\" src=\"https:\/\/content.embl.org\/sites\/default\/files\/styles\/medium\/public\/06-2026\/EMBL_EBI-logo.png?itok=wTzifBwt\" alt=\"SAS\">\n          <\/a>\n        \n                          <h3 class=\"vf-summary__title\">\n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/sas\">SAS<\/a>\n                      <\/h3>\n        \n                                          <p class=\"vf-summary__text\">\n            Annotation of protein sequence with structural info from similar proteins in the PDB\n          <\/p>\n              <\/article>\n          <article class=\"vf-summary vf-summary--has-image vf-summary-image\">\n                                \n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/sas\/\">\n            <img decoding=\"async\" class=\"vf-summary__image vf-summary__image--thumbnail\" src=\"https:\/\/content.embl.org\/sites\/default\/files\/styles\/medium\/public\/03-2025\/database-tool-icon_0-2-1.png?itok=q8BfADlO\" alt=\"SAS \u2013 Sequence Annotated by Structure\">\n          <\/a>\n        \n                          <h3 class=\"vf-summary__title\">\n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/sas\/\">SAS \u2013 Sequence Annotated by Structure<\/a>\n                      <\/h3>\n        \n                                          <p class=\"vf-summary__text\">\n            \nSAS is a tool for applying structural information to a given protein sequence. It uses FASTA to scan a given protein sequence against all the proteins of known 3D structure in the Protein Data Bank (PDB). The resultant multiple alignment can be coloured according to different structural features an\u2026\n          <\/p>\n              <\/article>\n          <article class=\"vf-summary vf-summary--has-image vf-summary-image\">\n                                \n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/cgi-bin\/valdar\/scorecons_server.pl\">\n            <img decoding=\"async\" class=\"vf-summary__image vf-summary__image--thumbnail\" src=\"https:\/\/content.embl.org\/sites\/default\/files\/styles\/medium\/public\/06-2026\/database-tool-icon_0-2-1.png?itok=ERcHjrr1\" alt=\"Scorecons\">\n          <\/a>\n        \n                          <h3 class=\"vf-summary__title\">\n                          <a class=\"vf-summary__link\" href=\"http:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/cgi-bin\/valdar\/scorecons_server.pl\">Scorecons<\/a>\n                      <\/h3>\n        \n                                          <p class=\"vf-summary__text\">\n            Scores residue conservation based on a given multiple sequence alignment\n          <\/p>\n              <\/article>\n          <article class=\"vf-summary vf-summary--has-image vf-summary-image\">\n                                \n                          <a class=\"vf-summary__link\" href=\"https:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/SurvCurv\/analyse.php\">\n            <img decoding=\"async\" class=\"vf-summary__image vf-summary__image--thumbnail\" src=\"https:\/\/content.embl.org\/sites\/default\/files\/styles\/medium\/public\/02-2026\/database-tool-icon_0-2-1.png?itok=sw8gNCwZ\" alt=\"SurvCurv \u2013 Analyse data\">\n          <\/a>\n        \n                          <h3 class=\"vf-summary__title\">\n                          <a class=\"vf-summary__link\" href=\"https:\/\/www.ebi.ac.uk\/thornton-srv\/databases\/SurvCurv\/analyse.php\">SurvCurv \u2013 Analyse data<\/a>\n                      <\/h3>\n        \n                                          <p class=\"vf-summary__text\">\n            Survival and other incident curves\n          <\/p>\n              <\/article>\n      <\/div>\n  <\/div>\n  <div><\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":6,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"embl_taxonomy":[],"class_list":["post-15","page","type-page","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"_links":{"self":[{"href":"https:\/\/www.ebi.ac.uk\/research\/thornton\/wp-json\/wp\/v2\/pages\/15","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ebi.ac.uk\/research\/thornton\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ebi.ac.uk\/research\/thornton\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/research\/thornton\/wp-json\/wp\/v2\/users\/6"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/research\/thornton\/wp-json\/wp\/v2\/comments?post=15"}],"version-history":[{"count":12,"href":"https:\/\/www.ebi.ac.uk\/research\/thornton\/wp-json\/wp\/v2\/pages\/15\/revisions"}],"predecessor-version":[{"id":13575,"href":"https:\/\/www.ebi.ac.uk\/research\/thornton\/wp-json\/wp\/v2\/pages\/15\/revisions\/13575"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/research\/thornton\/wp-json\/wp\/v2\/media?parent=15"}],"wp:term":[{"taxonomy":"embl_taxonomy","embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/research\/thornton\/wp-json\/wp\/v2\/embl_taxonomy?post=15"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}