Homology Modeling Sample Clauses

Homology Modeling. A homology model of mouse MD-2 was constructed by application of Prime v1.6 with the Maestro interface (Schrödinger, LLC) and by using the crystal structure of hMD-2 complexed with lipid IVa (PDB code 2E59; 79% sequence similarity)[38] as template. The resulting homology model was refined by backbone and side chain energy optimizations using the OPLS force field within Prime. A WHATIF analysis demonstrated very similar Z-scores between the mMD-2 homology model and the hMD-2 crystal structure in terms of 1st and 2nd generation packing quality, chi-1/chi-2 rotamer normality, and backbone conformation.
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Homology Modeling. Up to now, the crystal structure of human TLR4 is a hybrid one, which contains a part of the human TLR4 (N-terminal) and another LRR protein TV3. (PDB code: 2Z65) This incomplete human TLR4 structure could not be used in protein-protein docking. As a result, a homology model of the whole human TLR4 structure based on mouse TLR4 is required. Sequences were aligned with CLUSTALW.[46] Homology modeling of human TLR4 sequence to template (mouse TLR4) was performed using the application Prime v 2.0 within the Maestro interface (Schrödinger, LLC). The homology model was refined by backbone and side chain energy optimization using the OPLS force field within Prime. The resulting model of human TLR4 was evaluated by PROCHECK. MOLCAD, within SYBYL v 7.0 (Tripos, Inc.), was used to define Fast Xxxxxxxx van der Waals surfaces to which electrostatic (Tripos force field) and lipophilic [71] properties were mapped for this protein model.

Related to Homology Modeling

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  • DEVELOPMENT OR ASSISTANCE IN DEVELOPMENT OF SPECIFICATIONS REQUIREMENTS/ STATEMENTS OF WORK Firms and/or individuals that assisted in the development or drafting of the specifications, requirements, statements of work, or solicitation documents contained herein are excluded from competing for this solicitation. This shall not be applicable to firms and/or individuals providing responses to a publicly posted Request for Information (RFI) associated with a solicitation.

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