{"id":3265,"date":"2024-02-13T05:40:49","date_gmt":"2024-02-13T05:40:49","guid":{"rendered":"https:\/\/apexbtic.icgeb.res.in\/btisnet\/?p=3265"},"modified":"2024-02-13T05:55:37","modified_gmt":"2024-02-13T05:55:37","slug":"dsdbase2-0-ncbs-bangalore","status":"publish","type":"post","link":"https:\/\/apexbtic.icgeb.res.in\/btisnet\/dsdbase2-0-ncbs-bangalore\/","title":{"rendered":"DSDBASE2.0, NCBS Bangalore"},"content":{"rendered":"\n<p>DSDBASE is a database on disulphide bonds in proteins that provides information on native disulphides and those which are stereochemically possible between pairs of residues in a protein.<\/p>\n\n\n\n<p>One of the potential uses of such a disulphide database is to&nbsp;<a href=\"http:\/\/caps.ncbs.res.in\/cgi-bin\/dsdbase2\/help.py?help=modip&amp;help_t=MODIP%20online%20Help\"><strong>design site-directed mutants<\/strong><\/a>&nbsp;in order to enhance the thermal stability of the protein in question. Another important application is to employ this database for proposing&nbsp;<a href=\"http:\/\/caps.ncbs.res.in\/cgi-bin\/dsdbase2\/help.py?help=dsd_modelling&amp;help_t=Modeling%20Peptides\"><strong>3D models of disulphide-rich polypeptides<\/strong><\/a>&nbsp;like toxins and small proteins by searching for sub-structural motifs which are compatible with the derived disulphide bond connectivity. The user can obtain information about disulphide bonds of a particular protein of interest or probe the database for multiple disulphide bonded systems of particular connectivity.<\/p>\n\n\n\n<p>The DSDBASE database has not only been updated to include 153,944 PDB entries, 216,096 native and 20,153,850 modelled disulphide bond segments, the current database provides resource to user-friendly search for multiple disulphide bond containing loops, along with annotation of their function using GO and active site residues. Further, it is now also possible to obtain three-dimensional models of disulphide-rich small proteins using an independent algorithm, RANMOD (Sowdhamini et al., 1993)that generates and examines random, but allowed backbone conformations to the polypeptide.<\/p>\n\n\n\n<p><strong>NEW FEATURES<\/strong><\/p>\n\n\n\n<ol>\n<li>DSDBASE is upgraded to search in PDB-Jan 2021 release.<\/li>\n\n\n\n<li>Peptide fragments of distinct loop sizes from various substructures at Non Redundant of 90% sequence identity is available for download.<\/li>\n\n\n\n<li><a href=\"http:\/\/caps.ncbs.res.in\/cgi-bin\/dsdbase2\/load_form.py?module_name=ranmod&amp;module_desc=RANMOD\">RANMOD<\/a>&nbsp;procedure to model peptides that are rich in disulphides bond is available.<\/li>\n\n\n\n<li>GO annotations for Biological processes and Molecular functions are provided for the PDB hits.<\/li>\n\n\n\n<li>User can go to a PDB hit belonging to specific class of enzymes.<\/li>\n\n\n\n<li>Enhanced user interface with contextual help and easy navigation.<\/li>\n<\/ol>\n\n\n\n<div class=\"wp-block-buttons is-layout-flex\">\n<div class=\"wp-block-button\"><a class=\"wp-block-button__link wp-element-button\" href=\"http:\/\/caps.ncbs.res.in\/dsdbase2\/\" target=\"_blank\" rel=\"noreferrer noopener\">Browse<\/a><\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>DSDBASE is a database on disulphide bonds in proteins that provides information on native disulphides and those which are stereochemically [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":3267,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"site-sidebar-layout":"default","site-content-layout":"","ast-site-content-layout":"","site-content-style":"default","site-sidebar-style":"default","ast-global-header-display":"","ast-banner-title-visibility":"","ast-main-header-display":"","ast-hfb-above-header-display":"","ast-hfb-below-header-display":"","ast-hfb-mobile-header-display":"","site-post-title":"","ast-breadcrumbs-content":"","ast-featured-img":"","footer-sml-layout":"","theme-transparent-header-meta":"","adv-header-id-meta":"","stick-header-meta":"","header-above-stick-meta":"","header-main-stick-meta":"","header-below-stick-meta":"","astra-migrate-meta-layouts":"default","ast-page-background-enabled":"default","ast-page-background-meta":{"desktop":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center 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