Free Offer of the Protein Structure Data of the SARS Virus

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、RNA Polymerase、Helicase 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
Data Name A B C
ORF 1ab 1ab 1ab
protein_id AAP13442.1 AAP13442.1 AAP13442.1

Proteinase Model conbined with a ligand
Reference : 1LVO
Ligand : involved in 1HPG

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
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
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
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
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

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