Alpha-carbon protein model

Demonstration: Go model

Usage:

1. Click "Load" to load a PDB structure.
2. Click "Start" to start a molecular dynamics simulation.
3. Change the termpeature to unfold/fold the protein.
4. Check "Wang-Landau" to perform an entropic sampling (terribly slow, sorry).
5. For larger balls representation: set "Ball size" to 3.0; for C_α trace only, set "Ball size" to 0.

Source Code

Download this applet: GoApp.java.

Note: when embedded in a webpage, the applet cannot download remote PDB due to Java security reasons. To enable this function, do either of the follows:

• Download a standalone application Go.jar, open a command-line window, type java -jar Go.jar
• Or (Linux), download everything under this directory type make run

Explanation

The energy function has five contributions (see the reference):

1. Bonded: between residues i and i+1, ½ k_b (x - x_REF)².
2. Angle: among three residues i, i+1, and i+2, ½ k_a (θ - θ_REF)².
3. Dihedral: among residues i, i+1, i+2, and i+3, k_d1[1 - cos(φ)] + k_d3[1 - cos(3 φ)].
4. Nonbonded (contact^†): ε [5 (r_REF/r)¹² − 6 (r_REF/r)¹⁰].
5. Nonbonded (non-contact): ε (r_p / r)⁶).

^† Two residues are defined as contacts if their distance in the reference structure is less than rcutoff.

Reference

Cecilia Clementi, Hugh Nymeyer and Jose Nelson Onuchic, Topological and Energetic Factors: What Determines the Structural Details of the Transition State Ensemble and “En-route” Intermediates for Protein Folding? An Investigation for Small Globular Proteins, J. Mol. Biol. 298 937-953 (2000).