Dear all, RCSP PDB is delighted to announce the new 1D-3D Alignment Viewer. The viewer supports exploration of multiple sequence alignments (MSA) at sequence and structure levels for PDB experimental structures and Computed Structure Models (CSMs). Select proteins and/or residue regions from the MSA to view their 3D structures aligned in Mol*. And options to display (or hide) other polymeric chains or ligands.
Clusters of protein entity sequences (PDB experimental structures and CSMs) are calculated by sequence identity threshold or UniProt accession grouping. For each cluster, its MSA is computed using Clustal Omega <http://www.clustal.org/omega/> and displayed in the 1D-3D Alignment Viewer using specific color schemes. PDB protein sequence positions are represented in blue if residue was experimentally determined and gray if not. CSMs are colored according to their local pLDDT scores. To access this feature, click the 1D-3D Alignments link from any Group Summary or Group Sequence page (for an example, see the UniProt Group Summary for O95786 <https://www.rcsb.org/groups/summary/polymer_entity/O95786> or Sequence Identity 241_30 <https://www.rcsb.org/groups/summary/polymer_entity/241_30>). Group pages are available from Structure Summary pages (in the Entity Groups table) and Search Results (more documentation <https://www.rcsb.org/docs/grouping-structures/grouping-search-results>). Some examples: Iron hydrogenase 1 <https://www.rcsb.org/groups/3d-sequence/polymer_entity/P29166> GTPase HRas <https://www.rcsb.org/groups/3d-sequence/polymer_entity/P01112> Voltage-dependent calcium channel subunit alpha <https://www.rcsb.org/groups/3d-sequence/polymer_entity/P54289> Please, send any questions, concerns, or constructive feedback! Have a tremendous Christmas!!! -- Joan Segura Mora, Ph.D. Scientific Software Developer RCSB Protein Data Bank UCSD, San Diego Supercomputer Center 10100 Hopkins Drive, La Jolla, CA 92093-0505 E-mail: joan.seg...@rcsb.org, Tel: +1-858-246-0526 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
