Last Modified

   1 January 2020

Theoretical Organic Chemistry Nuclear Receptor Chemistry Structural Bioinformatics Rational Drug Design

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Technical Reports


Side Chain Rotamer Modeling program



Side Chain Rotamer Modeling of the Human Androgen Receptor (AR) Ligand-Binding Domain (LBD) Model Created Using the Human Progesterone Receptor (PR) LBD (1A28; Molecule B) as a Template Molecule.



The Side Chain Rotamer Modeling program precisely predicted the side-chain rotamers of the model in comparison with those of the corresponding crystal structure (except for the rotamer of Gln783 which results in a different main-chain conformation between hAR and hPR LBDs; see Figure). Since this result was based on the Faster method using single-point calculations, the rotamer prediction would be expected to additionally improve, when the geometry optimizations or the Conventional method of single-point calculations supported by the Side Chain Rotamer Modeling program are used. On the other hand, the Faster method was practical for a protein modeling in terms of the calculation times. Moreover, in the case of the database mode of the auto-rotamer search function, all searches were completed in a few minutes under the same conditions and this method led to the large shortening of the calculation times (92 % cut).

Although the present study was performed using HyperChem version 6.0.3, the all searches were completed at a few minutes under the same conditions when HyperChem version 7.5.1 was used.

Superposition between the Experimentally Solved and the Modeled hAR LBDs

Figure.  Superposition between the experimentally solved (blue) and the modeled (red) hAR LBDs.

Different residues (5 residues) between hAR and hPR LBDs (template) in the ligand-binding region (in 5 from ligand) are shown in this Figure. The 3D model of hAR LBD is shown in red and the crystal structure of hAR LBD is shown in blue. The superposed structures between the crystal structure and the preliminary 3D model (procedure 3, see below) of hAR LBDs are shown at the left-hand side ("Before"). The superposed structures between the crystal structure and the rotamer-modeled structure of hAR LBDs are shown at the right-hand side ("After").




Identity: 54.8 %

Non-identical Residues: 112

Residue Length: 249

Ligand: Metribolone (R1881)



1. Homology Modeling Program

   Model: A 3D model of hAR LBD was prepared using template 3D structure of hPR LBD.

2. HyperChem

   N- and C-Termini: zwitterion (INDO charges)

   Ligand: Metribolone was prepared (R1881) with MNDO/d atomic charges and Amber94 atom types.

3. HyperChem and Interface Selection Programs

   Force Field: Amber94

   Calculations: Tight geometry optimization (Gradient Error of 0.1) for all hydrogen atoms was performed.

4. Side Chain Rotamer Modeling Pro (Batch Calculations)

   Force Field: Amber94

   Faster Method, Redraw Display: ON, Others: Default

   In the case of the Auto-Rotamer Search Function:

      Torsion Angles : gamma = 60, delta = 60, epsilon = 60, zeta = 60

      Total Rotamers: 24,059 (24,059 Single-Point Calculations)

   In the case of the Auto-Rotamer Search Function based on the Rotamer Database:

      Rotamer Database version 1.0

      Total Rotamers: 2,111 (2,111 Single-Point Calculations)

5. HyperChem

   Calculations: Loose geometry optimization (Gradient Error of 1.0) for all side chain atoms was performed.

6. Restraints Program

   Final Coordinates: The coordinate of the above created 3D Model of hAR was used as a final coordinate.

   Restraints: Main chain and side chain heavy atoms ("All" Option) for both receptor and ligand were restrained to the final coordinate.

   Restraint Forces: Default

7. HyperChem

   Low-temperature (300 K, 3 ps) molecular dynamics annealing under the above restraint conditions was performed.


Used System

CPU: Intel Pentium4 3.06GHz (FSB 533 MHz; L2 512KB)

Memory: PC1066 1GB ECC

Chip Set: Intel I850E

SCSI: Ultra320

HDD: Ultra320 17GB

OS: Microsoft Windows XP Professional SP2

HyperChem: version 6.0.3





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