The program uses as input only a set of coordinate files in the PDB format. Unlike the previous version, it allows an automatic determination of transmembrane secondary structures without using any external software. The dipole moments and standard pKa values of different groups are included in the library of amino acid residues or directly in the PDB files for small molecules.
Optimized Transmembrane Protein Positioning
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Corresponding Organization :
Other organizations : University of Michigan–Ann Arbor
Protocol cited in 13 other protocols
Variable analysis
- Two rotation angles (φ, τ)
- One translation along the bilayer normal (d)
- Location of the hydrocarbon boundary (Z_HDC)
- Transfer energy (equation 19)
- Energy functions and parameters described in equations (1–42) and Tables S1, S3, S4
- Dipole moments and standard pKa values of different groups included in the library of amino acid residues or directly in the PDB files for small molecules
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