Gregory E. Sims Ph.D

Lawrence Berkeley National Lab\
1 Cyclotron Road Mail Stop Calvin Lab\
Berkeley, CA 94720-0350

Email: <gesims@lbl.gov>

<http://compgen.lbl.gov/~gsims>

Cell: (925) 628-3676

**Objective**

Currently seeking a research position in bioinformatics or computational
biology/chemistry, where my skills can be integrated into a focused team
of individuals working on solutions to pressing biological and clinical
problems.

**Education**

+-------------------+--------------------------------------------------+
| 2001 -- 2005      | University of California, Berkeley               |
|                   |                                                  |
|                   | Ph.D, Biophysics Graduate Group                  |
|                   |                                                  |
|                   | GPA: 3.95                                        |
+-------------------+--------------------------------------------------+
| 1997 -- 2001      | University of California, San Diego              |
|                   |                                                  |
|                   | B.S., Biochemistry/Chemistry with Honors         |
|                   |                                                  |
|                   | Areas of Focus: English Literature               |
|                   |                                                  |
|                   | Minor: Computer Science and Engineering          |
|                   |                                                  |
|                   | GPA: 3.90, *Summa Cum Laude*                     |
+-------------------+--------------------------------------------------+

**Awards and Honors**

> Golden Key Honor Society member
>
> Phi Beta Kappa Honor Society member
>
> Ruth L. Kirchstein National Research Service Award (2002-2004)
>
> Genomics Research Service Award (2004-2005)

Work Experience

+-----------+----------------------------------------------------------+
| 2002 -    | **Sung-Hou Kim Lab - UC Berkeley and Lawrence Berkeley   |
| Current   | National Lab**                                           |
|           |                                                          |
|           | **Post-doctoral Fellow -- Computational Genomics Group** |
|           |                                                          |
|           | Developed software for analyzing the conformational      |
|           | quality of theoretical and experimental protein models   |
|           | (HOPPscore)                                              |
|           |                                                          |
|           | Published 3D maps describing the protein fold universe,  |
|           | protein conformations, nucleic acid conformations and    |
|           | the drug-like chemical universe which have been          |
|           | recognized by the scientific media.                      |
|           |                                                          |
|           | Group account manager for NERSC supercomputer usage.     |
+-----------+----------------------------------------------------------+
| 1999-2001 | **Andrew McCammon Lab, UC San Diego**                    |
|           |                                                          |
|           | **Research Assistant III**                               |
|           |                                                          |
|           | Developed a theoretical model for a hexomeric complex of |
|           | *e. coli* enzymes in the *de novo* synthesis pathway of  |
|           | purine nucleotides with a rigid protein-protein docking  |
|           | algorithm.                                               |
|           |                                                          |
|           | Performed 50,000 CPU Hours of rigid protein-protein      |
|           | docking experiments on the San Diego Super Computer      |
|           | Center\'s (SDSC) machine, Blue Horizon.                  |
+-----------+----------------------------------------------------------+

**Professional Skills**

Extensive experience with bioinformatics tools including: BLAST,
PSI-BLAST, and remote homology detection.

Research software development in Linux, UNIX and Windows environments.

Experience administrating and configuring Linux systems.

Programming and software development in Perl, C/C++, Java, Awk, Python,
HTML.

Extensive study and use of biostatistics, multivariate analysis and
clustering. Familiar with statistical programming packages such as R,
S-plus.

Protein stability studies: Knowledge of protein denaturation (chemical
and temperature dependent), Circular Diochroism (CD), Differential
Scanning Calorimetry (DSC).

Research background in nucleic acid structure, function and dynamics.

Background in organic chemistry, chemical descriptors, and data mining.

**Publications**

Sims, G. E. 2005. Global Mapping and Multivariate Analysis of Protein
and Nucleic Acid Conformations. PhD Thesis. University of California,
Berkeley, Berkeley, California.

Gregory E. Sims, Sung-Hou Kim (2006) A method for evaluating the
structural quality of protein models using higher-order f-y pairs
scoring. *Proc. Nat. Acad. Sci.,* **103**, 4428-4432

Gregory E. Sims, In-Geol Choi, and Sung-Hou Kim (2005). Protein
Conformational Space in Higher Order Phi-psi Maps. *Proc. Nat. Acad.
Sci*. **102**, 618-621.

Gregory E. Sims and Sung-Hou Kim (2003). Global mapping of nucleic acid
conformational space:

Dinucleoside monophosphate conformations and transition pathways among
conformational classes.

*Nuc. Acids Res.* **31** (19): 5607-5616.

Jingtong Hou, Gregory E. Sims, Chao Zhang, and Sung-Hou Kim (2003). A
global representation of the protein fold space. *Proc. Nat. Acad.
Sci.*, **100** (5): 2386-2390.