A new pneumonia called SARS (Severe Acute Respiratory Syndrome) has been rampant particularly in Asian countries, and therefore many pharmaceutical companies and research institutes have been putting utmost efforts in developing antiviral drugs and vaccines to combat the disease.
In-Silico Sciences Inc, collaborating with Professor Umeyama (Kitasato University) has successfully predicted the structures of enzyme proteins such as Proteinase, RNA Polymerase and Helicase, that are involved in self-reproduction of SARS virus, based on the gene sequence of SARS virus determined by research institutions including the Centers for Disease Control and Prevention (CDC). Proteinase and RNA Polymerase are proteins to assist SARS virus in reproducing, thus can be targets for developing inhibitors.
In order to accelerate the studies to develop drugs to treat SARS, In-Silico Sciences Inc. has decided to offer the predicted structural data for free-of-charge.
Please send your request for the structural data (in PDB formats) of Proteinase$B!"(BRNA Polymerase$B!"(BHelicase from this form. Your name, affiliation, email address, phone/FAX numbers, and the purpose to get the data should be stated.
When you have any outcome (presentation in conferences, papers, or development of new drugs), you must cite the references below, and acknowledgment of the data obtained by PDFAMS software family, which is developed in the laboratory of Professor Hideaki Umeyama in School of Pharmaceutical Sciences, Kitasato University.
Ogata, K. and Umeyama, H. (2000) J. Mol. Graph. Model 18, 258-272, 305-306.
Iwadate, M., Ebisawa, K. and Umeyama, H. (2001) CBIJ 1, 136-148.
Predictied Structures Proteinase RNA Polymerase Helicase PDB IDs of the reference proteins 1LVO 1NB4 3PJR Visualizaions Data Name A B C ORF 1ab 1ab 1ab protein_id AAP13442.1 AAP13442.1 AAP13442.1 Used Program PDFAMS Pro PDFAMS Pro PDFAMS Pro
Proteinase Model conbined with a ligand
Reference : 1LVO
Ligand : involved in 1HPG
Visualization front view side view Data Name D ORF 1ab protein_id AAP13442.1 Used Program PDFAMS Ligand
Difference in the model structures between the alignments of the sequences and between the selection of references Visualization Different alignments in Proteinase modeling Different alignments and different references in RNA Polymerase modeling Data Name E F ORF 1a 1b protein_id AAP13439.1 AAP13440.1 Used Program PDFAMS Superior PDFAMS Superior
Results with different random seeds in Monte Carlo Method in Proteinase modeling Visualization 6 realization of Proteinase modeling 6 realization of Proteinase with a Ligand Data Name G H ORF 1a 1a protein_id AAP13439.1 AAP13439.1 Used Program PDFAMS Origin PDFAMS Ligand
Hexamer Structure of the Proteinase
Reference : 1LVO
Visualization Predicted Hexamer Structure Superposition with 1LVO Data name I ORF 1ab protein_id AAP13442.1 Used Program PDFAMS Complex
Proteinase Modeling by simultaneous usage of 6 subunits in 1LVO Visualization Superposition of the 6 subunits in 1LVO (Experimental) Proteinase Modeling with the reference structure that is an average of the 6 subunits in 1LVO Data Name J ORF 1ab protein_id AAP13442.1 Used Program PDFAMS multi
All the picture in above were produced with WebLab ViewerLite offered by MSI.