Pat Fleming Home Page

Patrick J. Fleming, Ph.D.

Yale University
Dept. of Molecular Biophysics and Biochemistry
P. O. Box 208114
New Haven, CT 06520-8114
(203)432-8957 Voice
(203)432-5688 Fax
Rm 355C J.W.Gibbs

Protein Packing and Occluded Surface Analysis
Structural Biology Software
Personal Interests

Protein Packing

An understanding of the folding and stability of proteins depends on an accurate evaluation of the interaction of buried atoms with each other. I work with Fred Richards to develop methods for calculation of atomic packing in the cores of protein models.

We are extending the concept of occluded surface as a means to estimate protein packing. Pat Fleming and "Pat" Pattabiraman originally developed the idea of occluded surface as a means to evaluate the native-like quality of protein structural models. Models of properly folded proteins have an occluded surface parameter that is within a narrow range. The occluded surface parameter for misfolded protein models is outside of this range.

This work is described in the following publication:
Pattabiraman, N., Ward, K.B. and Fleming, P.J. (1995) Occluded Molecular Surface: Analysis of Protein Packing, Journal of Molecular Recognition, 8:334-344

We have extended the OS analysis to include the calculation of a packing parameter that provides a residue by residue estimate of the packing of amino acid residues in protein models. The program, called OS, is described here.

An example of OS utility is the comparison of packing in ribonuclease at different temperatures. The structure of ribonuclease has been determined at temperatures from 98K to 320K by Tilton et al. [Biochemistry, 31, 2469, 1992]. A plot of the dependence of overall protein packing on temperature, determined using OS, is here. One may also compare residue by residue differences in packing. The residue packing differences between ribonuclease at 98K and 320K are plotted here. Notice that most individual residues have a greater packing value in the 98K structrue compared to the 320K structure. Neither the individual residue changes, nor the linear relationship of overall packing with temperature are decipherable by other methods of packing calculation.

Structural Biology Software

I am the webmaster for the Center for Structural Biology Web Site. This site contains userguides and worked examples for many of the software applications used in X-ray crystallography, NMR and molecular graphics. Although the site was created initially for students and fellows in the CSB core laboratory, we serve its contents to the WWW. Many other academic and corporate structural biology units now use these documents


A lecture on Surface Analysis of Proteins is available on-line.

Templates for preparing an on-line presentation in the format of the lecture above are also available. Download all files in this directory and read the readme.txt file for guidelines.


I have converted several of Fred Richard's programs to UNIX.

I wrote a program for plotting difference distance matrices in color and would appreciate feedback on it use.

Last Modified: Wednesday, 06-May-1998 16:28:17 EDT