What's New in 3DinSight

• Release of Transcriptional Regulation Portal. (Jan. 31, 2007)
  

• PROSITE patterns are updated. (Jan. 2007)
  

• Release of PDBnet. PDBnet is intended to provide a bird's-eye view of molecular organization in the structurome, and enables users to extract various kinds of information within the context of molecular interaction network. Users can start a search from the PDBnet interface or from the menu of 3DinSight. The search result page of 3DinSight is also directly linked to the corresponding PDB code in PDBnet. (Nov. 30, 2006)
  

• Gallery of biomolecules updated (about 230 images were added). (July, 2006)
  

• Release of ReadOUT server. This server calculates specificities (Z-scores) of direct readout (base-amino acid interaction) and indirect readout (DNA conformation and flexibility) for given protein-DNA complex structures. This server may be useful if you want to check the specificity of particular protein-DNA complex. (March, 2006)
  

• New version of ProNIT (Thermodynamic Database for Protein-Nucleic Acid Interactions) ProNIT 2.0 has been released. ProNIT current release, ProNIT 2.0, contains 4900 entries. Since we have deleted some data and have carried out major modifications, the entries of database are renumbered. We have provided a Mapping table, which relates the old and new entry numbers, to help the users. Please see the Release Notes to get more details about the current release.(July 25th, 2005)
  

• Cross-link with STING: ProTherm entries are linked to STING server, which provides comprehensive analysis of a relationship between protein sequence, structure, function and stability. PDB column in ProTherm is linked to STING sequence frame and Java Protein Dosssier (JPD), Mutation column is linked to JPD and STING Report, which is an exhaustive presentation of the structure/function descriptors for particular residues, and Secondary Structure column is linked to PDB Cartoon. Also, for given protein mutations searched within STING, each entry in STING Report is linked to available thermodynamic data in ProTherm. These cross-references would help users to analyze the relationship between structure and thermodynamics of proteins. (July 15, 2005)

• Gallery of biomolecules updated (about 370 images were added). (May, 2005)

• Disease Database updated: We have updated the Disease Database. (Feb.,2005)

• Gallery of biomolecules updated (about 400 images were added). (May 26, 2004)

• CHIME Viewer: CHIME was added for viewing 3D structures. A simple menu was provided to facilitate easy manipulation (display type, color, label, etc.) of images. (Apr. 7, 2004)
  

• Disease Database updated: We have updated the Disease Database. We also added Gene Name in the database. and it can be searched (Mar. 1, 2004)
  

• Sequence similarity search for PDB entries: A sequence similarity search can be launched from each entry screen of 3DinSight. A FASTA search result will be shown with a list of linked PDB entries with similar sequence. (Feb. 27, 2004)
  

• Version 4 of ProTherm Protein Thermodynamic Database: This version contains more than 15,000 thermodynamic data for proteins and mutants. (Dec. 11, 2003)
  

• Viewing ASA (Accessible Surface Area) of proteins (June 16, 2003)
  

  • We have implemented a tool, "ASAview", for viewing accessible surface area of each amino adcid residue of protein. The ASAView is linked from each PDB entry page after searching 3SinSight.

• Update of ProNIT: Thermodynamic Database for Protein-Nucleic Acid Interactions is updated: The database now contains more than 3,000 interaction data. (Jan. 21, 2003)
  

• Release of beta version of ProLINT, Protein-Ligand Interaction Database (Jan. 9, 2003).
  

  • This is the Web-version of the original ProLINT, and this beta version contains 11,079 experimental data on the interaction between kinases/proteases and ligands. The search interface is based on simple text-based queries. We will implement more advanced search interface and provide more links in the next version.

• In the Database of Base-Amino Acid Interactions, wild card can be used for specifying Atom Name: * for a string of characters and ? for a character.(Sept. 17, 2002)

• Web page is updated. The first page includes a new quick search box, which covers all the text fields in main search menu (ENTRY (PDB code), HEADER, TITLE, COMPND, SOURCE and AUTHOR fields in PDB file). (Dec., 2001)

• Update of ProNIT: Thermodynamic Database for Protein-Nucleic Acid Interactions is updated. The database now contains about 2,000 data. (Oct., 2001)

• 3rd version of ProTherm: Thermodynamic Database for Proteins and Mutants is released. The number of entries has reached 10,000. Please see Statistics for more detail. (Oct., 2001)

• Disease-Related Mutations updated. (Sept., 2001)

• Release of ProNIT: Thermodynamic Database for Protein-Nucleic Acid Interactions(12/12/2000)

• Mapping Disease-Related Mutations on Structure (3/30/2000)

• Searching and Displaying Ligand Information (3/30/2000)

• Displaying Mutation Sites in ProTherm (10/22/99)

• Checking DNA Conformation and Specific Interactions in the DNA-Protein Complex from 3DinSight (5/21/99)

• Database of Base-Amino Acid Interactions (2/26/99)

• Hyperlink from RasMol to HTML (2/26/99)

• Modification to RasMol (2/26/99)

• Release of ProTherm: Thermodynamic Database for Proteins and Mutants (9/29/98)

• Protein-Nucleic Acid Complex Database (9/17/98)

• We support VRML 2.0 for viewing structures (5/29/98)

• Link to Thermodynamic Database of Proteins (5/12/98)

• Special database server for 3DinSight (5/12/98)

• Homology Search of your Sequences against PDB (8/14/97)

• Finding PROSITE motifs in your sequence (6/19/97)

• Interfaces for PIR and SWISS-PROT (6/13/97)

• Protein Mutant Database implemented (6/12/97)

• Amino-Acid Analysis (4/7/97)

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