{"id":17,"date":"2013-02-26T20:32:40","date_gmt":"2013-02-26T20:32:40","guid":{"rendered":"http:\/\/faculty.engineering.ucdavis.edu\/template\/?page_id=17"},"modified":"2014-09-05T20:17:05","modified_gmt":"2014-09-05T20:17:05","slug":"publications","status":"publish","type":"page","link":"https:\/\/faculty.engineering.ucdavis.edu\/koehl\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"

2014 (7)<\/span><\/h3>\n

<\/a><\/p>\n

V.\u00a0Weinreb, L.\u00a0Li, S.N. Chandrasekaran, P.\u00a0Koehl, M.\u00a0Delarue, and C.W. Carter.
\nDomain motion sensed by the d1 switch, a remote dynamic packing motif. J. Biol. Chem.<\/em>, 289:4367-4376, 2014.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl and J.\u00a0Hass. Automatic alignment of genus-zero surfaces. IEEE Trans. Pattern Anal. Mach. Intell.<\/em>, 36:466-478, 2014.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl, F.\u00a0Poitevin, H.\u00a0Orland, and M.\u00a0Delarue. Modified Poisson Boltzmann equations for characterizing biomolecular solvation. J. Theo. Comp. Chem.<\/em>, page 1440001, 2014.<\/p>\n

<\/a><\/p>\n

D.\u00a0R. Weiss and P.\u00a0Koehl. Morphing methods to visualize coarse-grained protein dynamics. Methods Mol. Biol.<\/em>, 1084, 2014.<\/p>\n

<\/a><\/p>\n

P.\u00a0Francis-Lyon and P.\u00a0Koehl. Protein side-chain modeling with a protein-dependent optimized rotamer library. Proteins: Struct. Func. Bioinfo.<\/em>, (in press, 2014).<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl. Mathematics’s role in the grand challenge of deciphering the molecular basis of life. Frontiers in biomolecular sciences<\/em>, (in press, 2014).<\/p>\n

<\/a><\/p>\n

F.\u00a0Xei, D.\u00a0Tong, W.\u00a0Lifeng, H.\u00a0Dayong, C.H. Steven, P.\u00a0Koehl, and L.\u00a0Lu.
\nIdentifying essential pairwise interactions in elastic network model
\nusing the alpha shape theory. J. Comp. Chem.<\/em>, (in press, 2014).<\/p>\n

2013 (8)<\/span><\/h3>\n

<\/a><\/p>\n

J.\u00a0Li, P.\u00a0Mach, and P.\u00a0Koehl.
\nMeasuring the shapes of macromolecules and why it matters. Comp. Struct. Biotech. J.<\/em>, (in press, 2013).<\/p>\n

<\/a><\/p>\n

B.\u00a0Babakasal, D.\u00a0D. Gae, J.\u00a0Li, J.\u00a0C. Lagarias, P.\u00a0Koehl and A.\u00a0J. Fisher.
\nHis74 conservation in the bilin reductase PcyA family reflects an important role in protein-substrate structure and dynamics. Biochim. Biophys. Acta<\/em>, 537: 233-242, 2013.<\/p>\n

<\/a><\/p>\n

P.\u00a0Mach and P.\u00a0Koehl. Capturing protein sequence-structure specificity using computational sequence design. Proteins: Struct. Func. Bioinfo.<\/em>, 81, 1556-1570, 2013.<\/p>\n

<\/a><\/p>\n

A.\u00a0Tsui, D.\u00a0Fenton, P.\u00a0Vuong, J.\u00a0Hass, P.\u00a0Koehl, N.\u00a0Amenta, D.\u00a0Coeurjolly,
\nC.\u00a0DeCarli, and O.\u00a0T. Carmichael. Globally optimal cortical surface matching with exact landmark correspondence. In Proc. Information Processing in Medical Imaging, IPMI 2013<\/em>, pages 487-498, 2013.<\/p>\n

<\/a><\/p>\n

H.\u00a0Fushing, H.\u00a0Wang, K.\u00a0VanderWaal, B.\u00a0McCowan, and P.\u00a0Koehl. Multi-scale clustering by building a robust and self correcting ultrametric topology on data points. PLoS One<\/em>, 8:e56259, 2013.<\/p>\n

<\/a><\/p>\n

L.\u00a0Sauguet, F.\u00a0Poitevin, S.\u00a0Murail, G.\u00a0Moraga, C.\u00a0van Renterghem, A.\u00a0W. Thompson, P.\u00a0Koehl, P.\u00a0J. Corringer, M.\u00a0Baaden, and M.\u00a0Delarue. Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels. EMBO J.<\/em>, 32:728-741, 2013.<\/p>\n

<\/a><\/p>\n

M.\u00a0R. Smaoui, F.\u00a0Poitevin, M.\u00a0Delarue, P.\u00a0Koehl, H.\u00a0Orland, and J.\u00a0Waldisp\u00fchl. Computational assembly of polymorphic amyloid fibrils reveals stable
\naggregates. Biophys. J.<\/em>, 104:683-693, 2013.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl and P.\u00a0R\u00f8gen. Extracting knowledge from protein structure geometry. Proteins: Struct. Func. Bioinfo.<\/em>, 81:841-851, 2013.<\/p>\n

2012 (5)<\/span><\/h3>\n

<\/a><\/p>\n

E.\u00a0DiLuccio and P.\u00a0Koehl. The H-factor as a novel quality metric for homology modeling. J. Clin. Bioinfo<\/em>, 2:18-26, 2012.<\/p>\n

<\/a><\/p>\n

E.\u00a0Kang and P.\u00a0Koehl. Identifying alpha-helices in proteins using the contact map and morphological operations. J. Korean Inst. Next Gen. Comput.<\/em>, 8:75-86, 2012.<\/p>\n

<\/a><\/p>\n

P.\u00a0Mach and P.\u00a0Koehl. An analytical method for computing atomic contact areas in
\nbiomolecules. J. Comp. Chem.<\/em>, 34:105-120, 2012.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl. Fast recursive computation of 3d geometric moments from surface
\nmeshes. IEEE Trans. Pattern Anal. Mach. Intell.<\/em>, 34:2158-2163,
\n2012.<\/p>\n

<\/a><\/p>\n

S.\u00a0Gu, P.\u00a0Koehl, J.\u00a0Hass, and N.\u00a0Amenta. Surface-histogram: A new shape descriptor for protein-protein docking. Proteins: Struct. Func. Bioinfo.<\/em>, 80:221-238, 2012.<\/p>\n

2011 (8)<\/span><\/h3>\n

<\/a><\/p>\n

L.\u00a0Miao, H.\u00a0Qin, P.\u00a0Koehl, and J.\u00a0Song. Selective and specific ion binding on proteins at physiologically-relevant concentrations. FEBS Lett.<\/em>, 585:3126-3132, 2011.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl, H.\u00a0Orland, and M.\u00a0Delarue. Adapting Poisson-Boltzmann to the self-consistent mean field theory: Application to protein side-chain modeling. J. Chem. Phys.<\/em>, 135:055104, 2011.<\/p>\n

<\/a><\/p>\n

P.\u00a0Mach and P.\u00a0Koehl. Geometric measures of large biomolecules: Surface, volume, and
\npockets. J. Comp. Chem.<\/em>, 32:3023-3038, 2011.<\/p>\n

<\/a><\/p>\n

C.\u00a0Hu, P.\u00a0Koehl, and N.\u00a0Max. PackHelix: A tool for helix-sheet packing during protein structure prediction. Proteins: Struct. Func. Bioinfo.<\/em>, 78:2828-2843, 2011.<\/p>\n

<\/a><\/p>\n

F.\u00a0Poitevin, H.\u00a0Orland, S.\u00a0Doniach, P.\u00a0Koehl, and M.\u00a0Delarue. AquaSAXS: A web server for computation and fitting of SAXS profiles with a non-uniform hydration layer. Nucl. Acids. Res.<\/em>, 39:W184-W189, 2011.<\/p>\n

<\/a><\/p>\n

X.\u00a0Shi and P.\u00a0Koehl. Adaptive skin meshes coarsening for biomolecular simulation.
\nComput. Aided Graph. Design<\/em>, 28:307-320, 2011.<\/p>\n

<\/a><\/p>\n

E.\u00a0DiLuccio and P.\u00a0Koehl. A quality metric for homology modeling: the H-factor.
\nBMC Bioinformatics<\/em>, 12:48, 2011.<\/p>\n

<\/a><\/p>\n

X.\u00a0Shi and P.\u00a0Koehl. Geometry and topology for modeling biomolecular surfaces. Far East J. Applied Math.<\/em>, 50:1-34, 2011.<\/p>\n

2010 (4)<\/span><\/h3>\n

<\/a><\/p>\n

P.\u00a0Francis-Lyon, S.\u00a0Gu, J.\u00a0Hass, N.\u00a0Amenta, and P.\u00a0Koehl. Sampling the conformation of protein surface residues for flexible protein docking. BMC Bioinformatics<\/em>, 11:575, 2010.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl and M.\u00a0Delarue. AQUASOL: an efficient solver for the dipolar Poisson-Boltzmann-Langevin equation. J. Chem. Phys.<\/em>, 132:064101, 2010.<\/p>\n

<\/a><\/p>\n

C.\u00a0Hu and P.\u00a0Koehl. Helix-sheet packing in proteins. Proteins: Struct. Func. Bioinfo.<\/em>, 78:1736-1747, 2010.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl. Protein structure prediction. In T.\u00a0Jue, editor, Biomolecular applications of Biophysics<\/em>, pages 1-34. Humana press, New York, NY, 2010.<\/p>\n

2009 (6)<\/span><\/h3>\n

<\/a><\/p>\n

P.\u00a0Koehl, H.\u00a0Orland, and M.\u00a0Delarue. Computing ion solvation free energies using the dipolar Poisson model. J. Phys. Chem. B.<\/em>, 113:5694-5697, 2009.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl, H.\u00a0Orland, and M.\u00a0Delarue. Beyond Poisson-Boltzmann: Modeling biomolecule-water and water-water interactions. Phys. Rev. Let.<\/em>, 102:087801, 2009.<\/p>\n

<\/a><\/p>\n

X.\u00a0Shi and P.\u00a0Koehl. Adaptive surface meshes coarsening with guaranteed quality and
\ntopology. In Proc. Comput. Graphics Inter. Conf.<\/em>, pages 53-61, 2009.<\/p>\n

<\/a><\/p>\n

P.\u00a0Laowanapiban, M.\u00a0Kapustina, C.\u00a0Vonrhein, M.\u00a0Delarue, P.\u00a0Koehl, and C.\u00a0W.\u00a0Carter Jr. Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations. Proc. Natl. Acad. Sci. (USA)<\/em>, 106:1790-1795, 2009.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl. Molecular force fields. In S.\u00a0Park and J.\u00a0Cochran, editors, Protein engineering and design<\/em>, pages 255-277. CRC Press, Boca Raton, Fl, 2009.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl, H.\u00a0Orland, and M.\u00a0Delarue. Solvation of ion pairs: The Poisson-Langevin model. In Proc. International Conf. Applied Phys. Math.<\/em>, pages 917-923, 2009.<\/p>\n

2008 (4)<\/span><\/h3>\n

<\/a><\/p>\n

A.\u00a0Azuara, H.\u00a0Orland, M.\u00a0Bon, P.\u00a0Koehl, and M.\u00a0Delarue. Incorporating dipolar solvents with variable density in Poisson-Boltzmann electrostatics. Biophys. J.<\/em>, 95:5587-5605, 2008.<\/p>\n

<\/a><\/p>\n

Q.\u00a0Le, G.\u00a0Pollastri, and P.\u00a0Koehl. Structural alphabets for protein structure classification: a comparison study. JMB<\/em>, 387:431-450, 2008.<\/p>\n

<\/a><\/p>\n

X.\u00a0Shi and P.\u00a0Koehl. The geometry behind numerical solvers of the Poisson-Boltzmann
\nequation. Commun. Comput. Phys.<\/em>, 3:1032-1050, 2008.<\/p>\n

<\/a><\/p>\n

V.\u00a0Natarajan, P.\u00a0Koehl, Y.\u00a0Wang, and B.\u00a0Hamann. Visual analysis of biomolecular surfaces. In Visualization in Medicine and Life Sciences<\/em>, pages 237-255,
\n2008.<\/p>\n

2007 (3)<\/span><\/h3>\n

<\/a><\/p>\n

S.\u00a0Gu, O.\u00a0Poch, B.\u00a0Hamann, and P.\u00a0Koehl.
\nA geometric representation of protein sequences. In IEEE International Conf. Biol. Medicine<\/em>, pages 135-142, 2007.<\/p>\n

<\/a><\/p>\n

F.\u00a0Chalmel, T.\u00a0Leveillard, C.\u00a0Jaillard, A.\u00a0Lardenois, N.\u00a0Berdugo, E.\u00a0Morel, P.\u00a0Koehl, G.\u00a0Lambrou, A.\u00a0Holmgren, J.\u00a0A. Sahel, and O.\u00a0Poch. Rod-derived cone viability factor-2 is a novel bifunctional thioredoxin like protein with therapeutic potential. BMC Molec. Biol.<\/em>, 8:74-85, 2007.<\/p>\n

<\/a><\/p>\n

J.\u00a0Franklin, P.\u00a0Koehl, S.\u00a0Doniach, and M.\u00a0Delarue. Minactionpath: maximum likelihood trajectory for large-scale structural transitions in a coarse grained locally harmonic energy landscape.Nucl. Acids. Res.<\/em>, 35:V477-W482, 2007.<\/p>\n

2006 (6)<\/span><\/h3>\n

<\/a><\/p>\n

L.\u00a0McHale, X.\u00a0Tan, P.\u00a0Koehl, and R.\u00a0Michelmore. Plant NBS-LRR proteins: adaptable guards. Genome Biology<\/em>, 7:212, 2006.<\/p>\n

<\/a><\/p>\n

A.\u00a0Zomorodian, L.\u00a0Guibas, and P.\u00a0Koehl. Geometric filtering of pairwise atomic interactions applied to the design of efficient statistical potentials. Comput. Aided Graph. Design<\/em>, 23:531-544, 2006.<\/p>\n

<\/a><\/p>\n

E.\u00a0Lindahl, C.\u00a0Azuara, P.\u00a0Koehl, and M.\u00a0Delarue. NOMADRef: visualization, deformation, and refinement of macromolecular structures based on all-atom normal mode analysis. Nucl. Acids. Res.<\/em>, 34:W52-W56, 2006.<\/p>\n

<\/a><\/p>\n

C.\u00a0Azuara, E.\u00a0Lindahl, P.\u00a0Koehl, H.\u00a0Orland, and M.\u00a0Delarue. PDB_Hydro. incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics. Nucl. Acids. Res.<\/em>, 34:W38-W42, 2006.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl. Protein structure classification. Rev. Comput. Chem.<\/em>, 22:1-56, 2006.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl. Electrostatics calculations: latest methodological advances. Curr. Opin. Struct. Biol.<\/em>, 16:142-151, 2006.<\/p>\n

2005 (6)<\/span><\/h3>\n

<\/a><\/p>\n

J.\u00a0D. Thompson, P.\u00a0Koehl, R.\u00a0Ripp, and O.\u00a0Poch. BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark. Proteins: Struct. Func. Genet.<\/em>, 61:127-136, 2005.<\/p>\n

<\/a><\/p>\n

J.\u00a0D. Thompson, S.\u00a0R. Holbrook, K.\u00a0Katoh, P.\u00a0Koehl, D.\u00a0Moras, E.\u00a0Westhof, and
\nO.\u00a0Poch. MAO: a multiple alignment ontology for nucleic acid and protein
\nsequences. Nucl. Acids. Res.<\/em>, 33:4164-4171, 2005.<\/p>\n

<\/a><\/p>\n

H.\u00a0Edelsbrunner and P.\u00a0Koehl. The geometry of biomolecular solvation. MSRI Publications<\/em>, 52:243-275, 2005.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl. Relaxed specificity in aromatic prenyltransferases. Nature Chem. Biol.<\/em>, 1:71-72, 2005.<\/p>\n

<\/a><\/p>\n

R.\u00a0Kolodny, L.\u00a0Guibas, M.\u00a0Levitt, and P.\u00a0Koehl. Inverse kinematics in biology: the protein loop closure problem. Int. J. Robot. Res.<\/em>, 24:151-163, 2005.<\/p>\n

<\/a><\/p>\n

R.\u00a0Kolodny, P.\u00a0Koehl, and M.\u00a0Levitt. Comprehensive evaluation of protein structure alignment methods: Scoring by geometric measures. J. Mol. Biol.<\/em>, 346:1173-1188, 2005.<\/p>\n

2004 (3)<\/span><\/h3>\n

<\/a><\/p>\n

C.\u00a0Birck, L.\u00a0Damian, C.\u00a0Marty-Detraves, A.\u00a0Lougarre, C.\u00a0Shulze Briese, P.\u00a0Koehl, A.\u00a0Fournie, L.\u00a0Paquereau, and J.\u00a0P. Samama. A new lectin family with structure similarity to actinoporins revealed by the crystal structure of Xerocomus chrysenteron<\/i> lectin XCL. J. Mol. Biol.<\/em>, 344:1409-1420, 2004.<\/p>\n

<\/a><\/p>\n

R.\u00a0Bryant, H.\u00a0Edelsbrunner, P.\u00a0Koehl, and M.\u00a0Levitt. The weighted area derivative of a space filling diagram. Discrete Comput. Geom.<\/em>, 32:293-308, 2004.<\/p>\n

<\/a><\/p>\n

J.\u00a0M. Chandonia, N.\u00a0S. Walker, L.\u00a0L. Conte, P.\u00a0Koehl, M.\u00a0Levitt, and S.\u00a0E.
\nBrenner. Astral compendium enhancements. Nucl. Acids. Res.<\/em>, 32:D189-D192, 2004.<\/p>\n

2003 (1)<\/span><\/h3>\n

<\/a><\/p>\n

H.\u00a0Edelsbrunner and P.\u00a0Koehl. The weighted volume derivative of a space filling diagram. Proc. Natl. Acad. Sci. (USA)<\/em>, 100:2203-2208, 2003.<\/p>\n

2002 (7)<\/span><\/h3>\n

<\/a><\/p>\n

P.\u00a0Koehl and M.\u00a0Levitt. Sequence variations within protein families are linearly related to structural variations. J. Mol. Biol.<\/em>, 323:551-562, 2002.<\/p>\n

<\/a><\/p>\n

R.\u00a0Kolodny, P.\u00a0Koehl, L.\u00a0Guibas, and M.\u00a0Levitt. Small libraries of protein fragments model native protein structures accurately. J. Mol. Biol.<\/em>, 323:297-307, 2002.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl and M.\u00a0Levitt. Protein topology and stability define the space of allowed sequences. Proc. Natl. Acad. Sci. (USA)<\/em>, 99:1280-1285, 2002.<\/p>\n

<\/a><\/p>\n

J.\u00a0M. Chandonia, N.\u00a0S. Walker, L.\u00a0L. Conte, P.\u00a0Koehl, M.\u00a0Levitt, and S.\u00a0E. Brenner. Astral compendium enhancements. Nucl. Acids. Res.<\/em>, 30:260-263, 2002.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl and M.\u00a0Levitt. Improved recognition of native-like protein structures using a family of designed sequences. Proc. Natl. Acad. Sci. (USA)<\/em>, 99:691-696, 2002.<\/p>\n

<\/a><\/p>\n

P.\u00a0Agarwal, L.\u00a0Guibas, H.\u00a0Edelsbrunner, J.\u00a0Erickson, M.\u00a0Isard, S.\u00a0Har-Paled, J.\u00a0Hershberger, C.\u00a0Jensen, L.\u00a0Kavraki, P.\u00a0Koehl, M.\u00a0Lin, D.\u00a0Manocha, D.\u00a0Metaxas, B.\u00a0Mirtich, D.\u00a0Mount, S.\u00a0Muthukrishnan, D.\u00a0Pai, E.\u00a0Sacks, J.\u00a0Snoeyink, S.\u00a0Suri, and O.\u00a0Wolfson. Algorithmic issues in modeling motion. ACM Computing surveys<\/em>, 34:550-572, 2002.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl. Recent progress in computational protein design. In M.\u00a0Gromiha and S.\u00a0Selvaraj, editors, Protein folding, stability, and design<\/em>, pages 307-324. Research Signpost, Trivvendrum, India, 2002.<\/p>\n

2001 (4)<\/span><\/h3>\n

<\/a><\/p>\n

J.\u00a0E. Wedeking, C.\u00a0B. Trame, M.\u00a0Dorywalska, P.\u00a0Koehl, T.\u00a0M. Rasche, M.\u00a0McKee, D.\u00a0Fitzgerald, R.\u00a0J. Collier, and D.\u00a0B. McKay. Refined crystallographic structure of pseudomonas aeruginosa exotoxin a and its implications for the molecular mechanism of toxicity. J. Mol. Biol.<\/em>, 314:823-837, 2001.<\/p>\n

<\/a><\/p>\n

P.\u00a0Rabier, B.\u00a0Kieffer, P.\u00a0Koehl, and J.\u00a0F. Lef\u00e8vre. Fast measurements of heteronuclear relaxation: frequency domain analysis of NMR accordion spectroscopy. Mag. Res. Chem.<\/em>, 39:447-456, 2001.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl and M.\u00a0Levitt. De novo protein design. In O.\u00a0Jardetzky and M.\u00a0D. Finucane, editors, NATO ASI Series vol. 315<\/em>, pages 57-75. Plenum press, New York, NY, 2001.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl. Protein structure similarities. Curr. Opin. Struct. Biol.<\/em>, 11:348-353, 2001.<\/p>\n

2000 (2)<\/span><\/h3>\n

<\/a><\/p>\n

R.\u00a0Samudrala, E.\u00a0S. Huang, P.\u00a0Koehl, and M.\u00a0Levitt. Constructing side-chains on near native main chains for ab initio protein structure prediction. Prot. Eng.<\/em>, 13:453-457, 2000.<\/p>\n

<\/a><\/p>\n

S.\u00a0E. Brenner, P.\u00a0Koehl, and M.\u00a0Levitt. The Astral compendium for protein structure and sequence analysis. Nucl. Acids. Res.<\/em>, 28:254-256, 2000.<\/p>\n

1999 (6)<\/span><\/h3>\n

<\/a><\/p>\n

P.\u00a0Koehl and M.\u00a0Levitt. De novo protein design. I. in search of stability and specificity. J. Mol. Biol.<\/em>, 293:1161-1181, 1999.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl and M.\u00a0Levitt. De novo protein design. II. plasticity of protein sequences.
\nJ. Mol. Biol.<\/em>, 293:1182-1193, 1999.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl and M.\u00a0Levitt. Structure-based conformational preferences of amino acids. Proc. Natl. Acad. Sci. (USA)<\/em>, 96:12524-12529, 1999.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl. Linear prediction spectral analysis of NMR data. Progress in NMR spectroscopy<\/em>, 34:257-299, 1999.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl and M.\u00a0Levitt. A brighter future for protein structure prediction. Nature Struct. Biol.<\/em>, 6:108-111, 1999.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl and M.\u00a0Levitt. Theory and simulation: Can theory challenge experiment? Curr. Opin. Struct. Biol.<\/em>, 9:155-156, 1999.<\/p>\n

1998 (3)<\/span><\/h3>\n

<\/a><\/p>\n

E.\u00a0S. Huang, P.\u00a0Koehl, M.\u00a0Levitt, R.\u00a0V. Pappu, and J.\u00a0W. Ponder. Accuracy of side-chain prediction upon near-native protein backbones generated by ab-initio folding methods. Proteins: Struct. Func. Genet.<\/em>, 33:204-217, 1998.<\/p>\n

<\/a><\/p>\n

E.\u00a0Furuichi and P.\u00a0Koehl. Influence of protein structure database on the predictive power of statistical pair potentials. Proteins: Struct. Func. Genet.<\/em>, 31:139-149, 1998.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl and M.\u00a0Delarue. Building protein lattice models using self consistent mean field theory. J. Chem. Phys.<\/em>, 108:9540-9549, 1998.<\/p>\n

1997 (2)<\/span><\/h3>\n

<\/a><\/p>\n

P.\u00a0Koehl and M.\u00a0Delarue. The native sequence determines sidechain packing in a protein, but does optimal sidechain packing determine the native sequence? In Proc. Pacific Symp. Biocomputing<\/em>, pages 198-209, 1997.<\/p>\n

<\/a><\/p>\n

M.\u00a0Delarue and P.\u00a0Koehl. The inverse protein folding problem: self consistent mean field optimization of a structure specific mutation matrix. In Proc. Pacific Symp. Biocomputing<\/em>, pages 109-121, 1997.<\/p>\n

1996 (2)<\/span><\/h3>\n

<\/a><\/p>\n

S.\u00a0Sunada, N.\u00a0Go, and P.\u00a0Koehl. Calculation of NMR order parameters in proteins by normal mode analysis. J. Chem. Phys.<\/em>, 104:4768-4775, 1996.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl and M.\u00a0Delarue. Mean field minimization methods for biological macromolecules. Curr. Opin. Struct. Biol.<\/em>, 2:222-226, 1996.<\/p>\n

1995 (5)<\/span><\/h3>\n

<\/a><\/p>\n

P.\u00a0Koehl, C.\u00a0Ling, and J.\u00a0F. Lef\u00e8vre. Automatic phase correction of NMR spectra: statistics and limits. J. Chim. Phys.<\/em>, 92:1929-1938, 1995.<\/p>\n

<\/a><\/p>\n

M.\u00a0Delarue and P.\u00a0Koehl. Atomic environment energies in proteins defined from statistics of accessible and contact surface areas. J. Mol. Biol.<\/em>, 249:675-690, 1995.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl and M.\u00a0Delarue. A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modeling. Nature Struct. Biol.<\/em>, 2:163-170, 1995.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl and J.\u00a0F. Lef\u00e8vre. Relaxation matrix refinement: Nucleic acids. In D.\u00a0M. Grant and R.\u00a0K. Harris, editors, Encyclopedia of Nuclear Magnetic Resonance<\/em>. Wiley, Chichester, England, 1995.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl and M.\u00a0Delarue. Modeling side-chain conformation in proteins: a self consistent mean field approach. In M.\u00a0Geisow and R.\u00a0Epton, editors, Protein Engineering and Complementary Technologies<\/em>, pages 31-34. Mayflower Worldwide Ltd, Birmingham, England, 1995.<\/p>\n

1994 (6)<\/span><\/h3>\n

<\/a><\/p>\n

G.\u00a0Mer, C.\u00a0Kellenberger, P.\u00a0Koehl, R.\u00a0Stote, O.\u00a0Sorokine, A.\u00a0Van Dorsselaer, B.\u00a0Luu, H.\u00a0Hietter, and J.\u00a0F. Lef\u00e8vre. Disulphide bridge pairing and solution structure by 1H NMR of PMPD2, a 35 residue peptide isolated from Locusta migratoria<\/i>. Biochemistry<\/em>, 33:15397-15409, 1994.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl and M.\u00a0Delarue. Polar and non-polar atomic environments in the protein core: implications for folding and binding. Proteins: Struct. Func. Genet.<\/em>, 20:264-278, 1994.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl, C.\u00a0Ling, and J.\u00a0F. Lef\u00e8vre. Oversampling improves linear prediction quantification of magnetic resonance spectral parameters. J. Chim. Phys.<\/em>, 91:595-606, 1994.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl and M.\u00a0Delarue. Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy. J. Mol. Biol.<\/em>, 239:249-275, 1994.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl, C.\u00a0Ling, and J.\u00a0F. Lef\u00e8vre. Linear prediction quantification of magnetic resonance spectral parameters: statistics and limits. J. Magn. Reson.<\/em>, A109:32-40, 1994.<\/p>\n

<\/a><\/p>\n

G.\u00a0Mohn, P.\u00a0Koehl, H.\u00a0Budzikiewicz, and J.\u00a0F. Lef\u00e8vre. Solution structure of pyoverdin GM-II. Biochemistry<\/em>, 33:2843-2851, 1994.<\/p>\n

1993 (2)<\/span><\/h3>\n

<\/a><\/p>\n

B.\u00a0Bersch, P.\u00a0Koehl, Y.\u00a0Nakatani, G.\u00a0Ourisson, and A.\u00a0Milon. 1H nuclear magnetic resonance determination of the membrane-bound conformation of senktide, a highly selective neurokinin B agonist. J. Biol. NMR<\/em>, 3:91-112, 1993.<\/p>\n

<\/a><\/p>\n

B.\u00a0Kieffer, P.\u00a0Koehl, S.\u00a0Plaue, and J.\u00a0F. Lef\u00e8vre. Structural and dynamic studies of two antigenic loops from haemagglutinin: a relaxation matrix approach. J. Biol. NMR<\/em>, 3:91-112, 1993.<\/p>\n

1992 (3)<\/span><\/h3>\n

<\/a><\/p>\n

B.\u00a0Kieffer, P.\u00a0Koehl, and J.\u00a0F. Lef\u00e8vre. Modeling the dynamic of an antigenic peptide using NMR data. Biochimie<\/em>, 74:815-824, 1992.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl, B.\u00a0Kieffer, and J.\u00a0F. Lef\u00e8vre. Computer-assisted assignment of biological macromolecule NMR spectra. J. Chim. Phys.<\/em>, 89:135-146, 1992.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl, J.\u00a0F. Lef\u00e8vre, and O.\u00a0Jardetzky. Computing the geometry of a molecule in dihedral angle space using NMR-derived constraints: a new algorithm based on optimal filtering.J. Mol. Biol.<\/em>, 223:299-315, 1992.<\/p>\n

1986-1991 (9)<\/span><\/h3>\n

<\/a><\/p>\n

P.\u00a0Koehl, D.\u00a0Burnouf, and R.\u00a0P.\u00a0P. Fuchs. Mutagenesis induced by a single acetylaminofluorene adduct within the nari site is position dependent. In P.\u00a0C. Howard, S.\u00a0S. Hecht, and F.\u00a0A. Beland, editors, Nitroarenes: Occurrence, Metabolism and Biological Impact<\/em>, pages 105-112. Plenum Press, New York, NY, 1991.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl and J.\u00a0F. Lef\u00e8vre. The relaxation matrix reconstructed from an incomplete set of 2D-NOE data: Statistics and limits. Bull. Magn. Reson.<\/em>, 12:23-29, 1990.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl and J.\u00a0F. Lef\u00e8vre. The reconstruction of the relaxation matrix from an incomplete set of nuclear Overhauser effects. J. Magn. Reson.<\/em>, 87:565-583, 1990.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl, B.\u00a0Kieffer, and J.\u00a0F. Lef\u00e8vre. The dynamics of oligonucleotides and peptides determined by proton NMR. In O.\u00a0Jardetzky, editor, NATO ASI Series vol. 183<\/em>, pages 139-154. Plenum press, New York, NY, 1990.<\/p>\n

<\/a><\/p>\n

D.\u00a0Burnouf, P.\u00a0Koehl, and R.\u00a0P.\u00a0P. Fuchs. Position of a single acetylaminofluorene adduct within a mutational hot spot is critical for the related mutagenic event. In Y.\u00a0Kuroda, D.\u00a0M. Shankel, and M.\u00a0D. Waters, editors, Antimutagenesis and Anticarcinogenesis Mechanisms II<\/em>, pages 277-288. Plenum Press, New York, NY, 1990.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl, P.\u00a0Valladier, J.\u00a0F. Lef\u00e8vre, and R.\u00a0P.\u00a0P. Fuchs. Strong structural effect of the position of a single acetylaminofluorene adduct within a mutation hot spot. Nucl. Acids. Res.<\/em>, 17:9531-9541, 1989.<\/p>\n

<\/a><\/p>\n

D.\u00a0Burnouf, P.\u00a0Koehl, and R.\u00a0P.\u00a0P. Fuchs. Single adduct mutagenesis : Strong effect of the position of a single acetylaminofluorene adduct within a mutation hot spot. Proc. Natl. Acad. Sci. (USA)<\/em>, 86:4147-4151, 1989.<\/p>\n

<\/a><\/p>\n

P.\u00a0Koehl, D.\u00a0Burnouf, and R.\u00a0P.\u00a0P. Fuchs. Construction of plasmids containing a unique acetylaminofluorene adduct located within a mutation hot spot: A new probe for frameshift mutagenesis. J. Mol. Biol.<\/em>, 207:355-364, 1989.<\/p>\n

<\/a><\/p>\n

A.\u00a0Chatterjee, P.\u00a0Koehl, and J.\u00a0L. Magee. Theoretical consideration of the chemical pathways for radiation-induced strand breaks. Adv. Space Res.<\/em>, 6:97-105, 1986.<\/p>\n","protected":false},"excerpt":{"rendered":"

2014 (7) V.\u00a0Weinreb, L.\u00a0Li, S.N. Chandrasekaran, P.\u00a0Koehl, M.\u00a0Delarue, and C.W. Carter. Domain motion sensed by the d1 switch, a remote dynamic packing motif. J. Biol. Chem., 289:4367-4376, 2014. P.\u00a0Koehl and J.\u00a0Hass. Automatic alignment of genus-zero surfaces. IEEE Trans. Pattern Anal. Mach. Intell., 36:466-478, 2014. P.\u00a0Koehl, F.\u00a0Poitevin, H.\u00a0Orland, and M.\u00a0Delarue. Modified \u2026 Continue reading → <\/span><\/a><\/p>\n","protected":false},"author":3,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"open","template":"template-twocolumns-left.php","meta":{"inline_featured_image":false,"ngg_post_thumbnail":0,"footnotes":""},"class_list":["post-17","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/faculty.engineering.ucdavis.edu\/koehl\/wp-json\/wp\/v2\/pages\/17","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/faculty.engineering.ucdavis.edu\/koehl\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/faculty.engineering.ucdavis.edu\/koehl\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/faculty.engineering.ucdavis.edu\/koehl\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/faculty.engineering.ucdavis.edu\/koehl\/wp-json\/wp\/v2\/comments?post=17"}],"version-history":[{"count":13,"href":"https:\/\/faculty.engineering.ucdavis.edu\/koehl\/wp-json\/wp\/v2\/pages\/17\/revisions"}],"predecessor-version":[{"id":282,"href":"https:\/\/faculty.engineering.ucdavis.edu\/koehl\/wp-json\/wp\/v2\/pages\/17\/revisions\/282"}],"wp:attachment":[{"href":"https:\/\/faculty.engineering.ucdavis.edu\/koehl\/wp-json\/wp\/v2\/media?parent=17"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}