I am developing a small molecules database system. Now it has features as below:

  • 70888 small molecules
  • 95 protein receptors
  • 36 descriptors calculated by QikProp (Jorgensen's program)
  • can be searched by key words, descriptors
  • can be searched by substructure
  • can be searched by QSAR equation
  • can be searched by 3D pharmacore model (developping)
  • can be searched by docking (use DOCK4)
  • can be searched by Euclidean Distance
  • can be searched by Tanimoto Coefficient
  • can do logical operation between searching result set

BossGUI is a Graphics User Interface developped for BOSS - mento carlo simulation program developped by Prof. Jorgensen. BossGUI is writen by Java, it is assumed to run in all posssible opreating system. The user can do some Mento Carlo calculation via BossGUI, and BossGUI has good communication to Rasmol. therefore, all molecules can be displayed graphically. Because molecule file format convertion program - autozmat is integreted in BOSS. It is very easy to show molecule file that rasmol can not recognize but autozmat can read.

You should ask Prof. Jorgensen for permission of using it.

 

I was involved in both building and maintainment of these servers:

I developed a new method to analyze residue-residue interaction in proteins by polymer statistics theory. I also analyzed in using the new method on Dali domain definition version3 and the PDB maintained in our PKUBIOS. The result contains a 20*20 residue-residue interaction matrix, 20 amino acid residue side chain apparent radius and residue-residue side chain center minimal and maximal distance.I constructed a potential function for evaluating protein structure by the parameters above, and I used Michael Levitt decoys set to test our new potential function. I found our potential function had very good performance even if I used the decoys set constructed by homology protein prediction technique.

BIND: A New Program to Estimate the Binding Free Energy of Protein-Protein Complex

Data Mining in Crystallography, 29th course, May, 1999

We proposed a new method to estimate the binding free energy of protein-protein complex with three-dimensional structure, and used an empirical score function to calculate the free energy, the function include terms to describe Van der Waals interaction, hydrogen bonding, desolvation, electrostatic interaction, side-chain entropy lost, hydrophobic interaction, and three terms coming from accessible surface including contact solvent accessible surface, hydrophobic accessible surface and hydrophilic accessible surface. The coefficients of each term are obtained by multivariate regression analysis of a training set of 29 protein-protein complexes, the correlation coefficient is 0.93. The final score function reproduced the binding free energies of the training set with a cross-validation deviation 5.4 kJ/mol. Finally, we can give estimation that how much free energy each aminoacid in the binding surface is constructed, then we know how to mutate the aminoacid sequence.

Modeling of Nylon Mixture

We developed an algorithm to predict the structure of Nylon crystal region via Nylon-6 crystal structure, then we applied this algorithm to construct Nylon-6,6 crystal region structure. We also constructed the possible structure of Nylon-6, Nylon-6,6 mixture of 1:1, 1:2, 2:1 proportion, and calculated the energy change of the blend procedure. Finally, we drew the conclusion: Nylon-6, Nylon-6,6 mixture is not stable. It is same as the experiment.

Molsee is a tcl/tk based program developed to control rasmol, which makes it ease to use rasmol. Use link below to read details about it.

Molsee: A tcl/tk based program to control Rasmol

 

  • MMLib: A c++ class library for molecular machenics
  • 2DAnalysis: A tcl/tk based program to draw a 2D graph for given data
  • BIND: A new program to predict the binding free energy of protein-protein complex
  • SimLinus: A program to predict protein tertiary structure from sequence (Use a hierarchical searching technique)
  • SP: A program to predict protein teriary structure from sequence (Use a hydrophobic potential)