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Gregory E. Sims, Ph.D.

Affiliations: 
2005 University of California, Berkeley, Berkeley, CA, United States 
Area:
Structural biology
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"Gregory Sims"
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Parents

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Sung-Hou Kim grad student 2005 UC Berkeley
 (Global mapping and multivariate analysis of protein and nucleic acid conformational spaces.)

Children

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Collaborators

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In-Geol Choi collaborator 2002-2007 UC Berkeley
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Publications

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Sims GE, Kim SH. (2011) Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs). Proceedings of the National Academy of Sciences of the United States of America. 108: 8329-34
Jun SR, Sims GE, Wu GA, et al. (2010) Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution. Proceedings of the National Academy of Sciences of the United States of America. 107: 133-8
Sims GE, Jun SR, Wu GA, et al. (2009) Whole-genome phylogeny of mammals: evolutionary information in genic and nongenic regions. Proceedings of the National Academy of Sciences of the United States of America. 106: 17077-82
Wu GA, Jun SR, Sims GE, et al. (2009) Whole-proteome phylogeny of large dsDNA virus families by an alignment-free method. Proceedings of the National Academy of Sciences of the United States of America. 106: 12826-31
Sims GE, Jun SR, Wu GA, et al. (2009) Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions. Proceedings of the National Academy of Sciences of the United States of America. 106: 2677-82
Sims GE, Kim SH. (2006) A method for evaluating the structural quality of protein models by using higher-order phi-psi pairs scoring. Proceedings of the National Academy of Sciences of the United States of America. 103: 4428-32
Sims GE, Choi IG, Kim SH. (2005) Protein conformational space in higher order phi-Psi maps. Proceedings of the National Academy of Sciences of the United States of America. 102: 618-21
Sims GE, Kim SH. (2003) Global mapping of nucleic acid conformational space: dinucleoside monophosphate conformations and transition pathways among conformational classes. Nucleic Acids Research. 31: 5607-16
Hou J, Sims GE, Zhang C, et al. (2003) A global representation of the protein fold space. Proceedings of the National Academy of Sciences of the United States of America. 100: 2386-90
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