This site is a fork of the original PRABI Geno3D server

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May 3rd, 2024: Geno3D updated (see NEWS).

May 2024
Updated PSI-BLAST command line option (Smith-Waterman alignments).
Fixed Template validation page: HTML code and missing template PDB code and multiple sequence alignment link when Structural overlap (Sov) parameter is computed.

March 2024
Updated Contact form to improve robustness against antispam filters.
Hardware and software upgraded. We apologize for service disruptions during first week of March.

February 2024
PDB 3-D coordinates, PDB SEQRES and Protein 3D sequences updated.
UniProt Knowledgebase updated (UniProtKB/Swiss-Prot+UniProtKB/TrEMBL 2024_01).

December 2023
Fixed broken NPSA link provided in pairwise alignment page (accessed from see alignment link in template selection table).

November 2023
PDB 3-D coordinates, PDB SEQRES and Protein 3D sequences updated.
UniProt Knowledgebase updated (UniProtKB/Swiss-Prot+UniProtKB/TrEMBL 2023_05).
Geno3D web form:
- added usage advice between [] for NPSA3DB and NPSA3D25 sequence databases
- added "2500" option for "Number of template to show" parameter
- added "BLOSUM50", "BLOSUM90" and "PAM250" options for "matrix" parameter
- decreased "Maximum number of passes to use in multipass version" from "2" to "1" to save CPU time and for query multi-domain protein

July 2023
PDB 3-D coordinates, PDB SEQRES and Protein 3D sequences updated.
UniProt Knowledgebase updated (2023_03).
Geno3D updated:
- increased number of non-standard groups (heterogen) supported
- fixed 'No page to display' message for report and valid files
- fixed missing RMSD, restraints and violation graphs

May 2023
Geno3D updated:
- fixed missing Procheck result in some cases
- fixed number and percentage of restraints violations displayed
- changed link name from jpeg to graph
- changed PNG images suffix from jpg to png
- updated some text and corrected typos in result pages

April 2023
This service was unavailable between April 19th and 30th following two power cuts in the city on April 19th and 23rd which affected a component of the network infrastructure. We apologize for the inconvenience caused.
Opening of this fork site with minor improvements that increase template identification and selection:
- two stages template search with PSI-BLAST+ 2.13.0 with UniProtKB clustered at 50+% identity
- UniProtKB and Protein Data Bank ENT file coordinate sequences updated
- added coverage to query column in template selection table

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