V. Weinreb, L. Li, S.N. Chandrasekaran, P. Koehl, M. Delarue, and C.W. Carter.
Domain motion sensed by the d1 switch, a remote dynamic packing motif. J. Biol. Chem., 289:4367-4376, 2014.
P. Koehl and J. Hass. Automatic alignment of genus-zero surfaces. IEEE Trans. Pattern Anal. Mach. Intell., 36:466-478, 2014.
P. Koehl, F. Poitevin, H. Orland, and M. Delarue. Modified Poisson Boltzmann equations for characterizing biomolecular solvation. J. Theo. Comp. Chem., page 1440001, 2014.
D. R. Weiss and P. Koehl. Morphing methods to visualize coarse-grained protein dynamics. Methods Mol. Biol., 1084, 2014.
P. Francis-Lyon and P. Koehl. Protein side-chain modeling with a protein-dependent optimized rotamer library. Proteins: Struct. Func. Bioinfo., (in press, 2014).
P. Koehl. Mathematics’s role in the grand challenge of deciphering the molecular basis of life. Frontiers in biomolecular sciences, (in press, 2014).
F. Xei, D. Tong, W. Lifeng, H. Dayong, C.H. Steven, P. Koehl, and L. Lu.
Identifying essential pairwise interactions in elastic network model
using the alpha shape theory. J. Comp. Chem., (in press, 2014).
J. Li, P. Mach, and P. Koehl.
Measuring the shapes of macromolecules and why it matters. Comp. Struct. Biotech. J., (in press, 2013).
B. Babakasal, D. D. Gae, J. Li, J. C. Lagarias, P. Koehl and A. J. Fisher.
His74 conservation in the bilin reductase PcyA family reflects an important role in protein-substrate structure and dynamics. Biochim. Biophys. Acta, 537: 233-242, 2013.
P. Mach and P. Koehl. Capturing protein sequence-structure specificity using computational sequence design. Proteins: Struct. Func. Bioinfo., 81, 1556-1570, 2013.
A. Tsui, D. Fenton, P. Vuong, J. Hass, P. Koehl, N. Amenta, D. Coeurjolly,
C. DeCarli, and O. T. Carmichael. Globally optimal cortical surface matching with exact landmark correspondence. In Proc. Information Processing in Medical Imaging, IPMI 2013, pages 487-498, 2013.
H. Fushing, H. Wang, K. VanderWaal, B. McCowan, and P. Koehl. Multi-scale clustering by building a robust and self correcting ultrametric topology on data points. PLoS One, 8:e56259, 2013.
L. Sauguet, F. Poitevin, S. Murail, G. Moraga, C. van Renterghem, A. W. Thompson, P. Koehl, P. J. Corringer, M. Baaden, and M. Delarue. Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels. EMBO J., 32:728-741, 2013.
M. R. Smaoui, F. Poitevin, M. Delarue, P. Koehl, H. Orland, and J. Waldispühl. Computational assembly of polymorphic amyloid fibrils reveals stable
aggregates. Biophys. J., 104:683-693, 2013.
P. Koehl and P. Røgen. Extracting knowledge from protein structure geometry. Proteins: Struct. Func. Bioinfo., 81:841-851, 2013.
E. DiLuccio and P. Koehl. The H-factor as a novel quality metric for homology modeling. J. Clin. Bioinfo, 2:18-26, 2012.
E. Kang and P. Koehl. Identifying alpha-helices in proteins using the contact map and morphological operations. J. Korean Inst. Next Gen. Comput., 8:75-86, 2012.
P. Mach and P. Koehl. An analytical method for computing atomic contact areas in
biomolecules. J. Comp. Chem., 34:105-120, 2012.
P. Koehl. Fast recursive computation of 3d geometric moments from surface
meshes. IEEE Trans. Pattern Anal. Mach. Intell., 34:2158-2163,
S. Gu, P. Koehl, J. Hass, and N. Amenta. Surface-histogram: A new shape descriptor for protein-protein docking. Proteins: Struct. Func. Bioinfo., 80:221-238, 2012.
L. Miao, H. Qin, P. Koehl, and J. Song. Selective and specific ion binding on proteins at physiologically-relevant concentrations. FEBS Lett., 585:3126-3132, 2011.
P. Koehl, H. Orland, and M. Delarue. Adapting Poisson-Boltzmann to the self-consistent mean field theory: Application to protein side-chain modeling. J. Chem. Phys., 135:055104, 2011.
P. Mach and P. Koehl. Geometric measures of large biomolecules: Surface, volume, and
pockets. J. Comp. Chem., 32:3023-3038, 2011.
C. Hu, P. Koehl, and N. Max. PackHelix: A tool for helix-sheet packing during protein structure prediction. Proteins: Struct. Func. Bioinfo., 78:2828-2843, 2011.
F. Poitevin, H. Orland, S. Doniach, P. Koehl, and M. Delarue. AquaSAXS: A web server for computation and fitting of SAXS profiles with a non-uniform hydration layer. Nucl. Acids. Res., 39:W184-W189, 2011.
X. Shi and P. Koehl. Adaptive skin meshes coarsening for biomolecular simulation.
Comput. Aided Graph. Design, 28:307-320, 2011.
E. DiLuccio and P. Koehl. A quality metric for homology modeling: the H-factor.
BMC Bioinformatics, 12:48, 2011.
X. Shi and P. Koehl. Geometry and topology for modeling biomolecular surfaces. Far East J. Applied Math., 50:1-34, 2011.
P. Francis-Lyon, S. Gu, J. Hass, N. Amenta, and P. Koehl. Sampling the conformation of protein surface residues for flexible protein docking. BMC Bioinformatics, 11:575, 2010.
P. Koehl and M. Delarue. AQUASOL: an efficient solver for the dipolar Poisson-Boltzmann-Langevin equation. J. Chem. Phys., 132:064101, 2010.
C. Hu and P. Koehl. Helix-sheet packing in proteins. Proteins: Struct. Func. Bioinfo., 78:1736-1747, 2010.
P. Koehl. Protein structure prediction. In T. Jue, editor, Biomolecular applications of Biophysics, pages 1-34. Humana press, New York, NY, 2010.
P. Koehl, H. Orland, and M. Delarue. Computing ion solvation free energies using the dipolar Poisson model. J. Phys. Chem. B., 113:5694-5697, 2009.
P. Koehl, H. Orland, and M. Delarue. Beyond Poisson-Boltzmann: Modeling biomolecule-water and water-water interactions. Phys. Rev. Let., 102:087801, 2009.
X. Shi and P. Koehl. Adaptive surface meshes coarsening with guaranteed quality and
topology. In Proc. Comput. Graphics Inter. Conf., pages 53-61, 2009.
P. Laowanapiban, M. Kapustina, C. Vonrhein, M. Delarue, P. Koehl, and C. W. Carter Jr. Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations. Proc. Natl. Acad. Sci. (USA), 106:1790-1795, 2009.
P. Koehl. Molecular force fields. In S. Park and J. Cochran, editors, Protein engineering and design, pages 255-277. CRC Press, Boca Raton, Fl, 2009.
P. Koehl, H. Orland, and M. Delarue. Solvation of ion pairs: The Poisson-Langevin model. In Proc. International Conf. Applied Phys. Math., pages 917-923, 2009.
A. Azuara, H. Orland, M. Bon, P. Koehl, and M. Delarue. Incorporating dipolar solvents with variable density in Poisson-Boltzmann electrostatics. Biophys. J., 95:5587-5605, 2008.
Q. Le, G. Pollastri, and P. Koehl. Structural alphabets for protein structure classification: a comparison study. JMB, 387:431-450, 2008.
X. Shi and P. Koehl. The geometry behind numerical solvers of the Poisson-Boltzmann
equation. Commun. Comput. Phys., 3:1032-1050, 2008.
V. Natarajan, P. Koehl, Y. Wang, and B. Hamann. Visual analysis of biomolecular surfaces. In Visualization in Medicine and Life Sciences, pages 237-255,
S. Gu, O. Poch, B. Hamann, and P. Koehl.
A geometric representation of protein sequences. In IEEE International Conf. Biol. Medicine, pages 135-142, 2007.
F. Chalmel, T. Leveillard, C. Jaillard, A. Lardenois, N. Berdugo, E. Morel, P. Koehl, G. Lambrou, A. Holmgren, J. A. Sahel, and O. Poch. Rod-derived cone viability factor-2 is a novel bifunctional thioredoxin like protein with therapeutic potential. BMC Molec. Biol., 8:74-85, 2007.
J. Franklin, P. Koehl, S. Doniach, and M. Delarue. Minactionpath: maximum likelihood trajectory for large-scale structural transitions in a coarse grained locally harmonic energy landscape.Nucl. Acids. Res., 35:V477-W482, 2007.
L. McHale, X. Tan, P. Koehl, and R. Michelmore. Plant NBS-LRR proteins: adaptable guards. Genome Biology, 7:212, 2006.
A. Zomorodian, L. Guibas, and P. Koehl. Geometric filtering of pairwise atomic interactions applied to the design of efficient statistical potentials. Comput. Aided Graph. Design, 23:531-544, 2006.
E. Lindahl, C. Azuara, P. Koehl, and M. Delarue. NOMADRef: visualization, deformation, and refinement of macromolecular structures based on all-atom normal mode analysis. Nucl. Acids. Res., 34:W52-W56, 2006.
C. Azuara, E. Lindahl, P. Koehl, H. Orland, and M. Delarue. PDB_Hydro. incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics. Nucl. Acids. Res., 34:W38-W42, 2006.
P. Koehl. Protein structure classification. Rev. Comput. Chem., 22:1-56, 2006.
P. Koehl. Electrostatics calculations: latest methodological advances. Curr. Opin. Struct. Biol., 16:142-151, 2006.
J. D. Thompson, P. Koehl, R. Ripp, and O. Poch. BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark. Proteins: Struct. Func. Genet., 61:127-136, 2005.
J. D. Thompson, S. R. Holbrook, K. Katoh, P. Koehl, D. Moras, E. Westhof, and
O. Poch. MAO: a multiple alignment ontology for nucleic acid and protein
sequences. Nucl. Acids. Res., 33:4164-4171, 2005.
H. Edelsbrunner and P. Koehl. The geometry of biomolecular solvation. MSRI Publications, 52:243-275, 2005.
P. Koehl. Relaxed specificity in aromatic prenyltransferases. Nature Chem. Biol., 1:71-72, 2005.
R. Kolodny, L. Guibas, M. Levitt, and P. Koehl. Inverse kinematics in biology: the protein loop closure problem. Int. J. Robot. Res., 24:151-163, 2005.
R. Kolodny, P. Koehl, and M. Levitt. Comprehensive evaluation of protein structure alignment methods: Scoring by geometric measures. J. Mol. Biol., 346:1173-1188, 2005.
C. Birck, L. Damian, C. Marty-Detraves, A. Lougarre, C. Shulze Briese, P. Koehl, A. Fournie, L. Paquereau, and J. P. Samama. A new lectin family with structure similarity to actinoporins revealed by the crystal structure of Xerocomus chrysenteron lectin XCL. J. Mol. Biol., 344:1409-1420, 2004.
R. Bryant, H. Edelsbrunner, P. Koehl, and M. Levitt. The weighted area derivative of a space filling diagram. Discrete Comput. Geom., 32:293-308, 2004.
J. M. Chandonia, N. S. Walker, L. L. Conte, P. Koehl, M. Levitt, and S. E.
Brenner. Astral compendium enhancements. Nucl. Acids. Res., 32:D189-D192, 2004.
H. Edelsbrunner and P. Koehl. The weighted volume derivative of a space filling diagram. Proc. Natl. Acad. Sci. (USA), 100:2203-2208, 2003.
P. Koehl and M. Levitt. Sequence variations within protein families are linearly related to structural variations. J. Mol. Biol., 323:551-562, 2002.
R. Kolodny, P. Koehl, L. Guibas, and M. Levitt. Small libraries of protein fragments model native protein structures accurately. J. Mol. Biol., 323:297-307, 2002.
P. Koehl and M. Levitt. Protein topology and stability define the space of allowed sequences. Proc. Natl. Acad. Sci. (USA), 99:1280-1285, 2002.
J. M. Chandonia, N. S. Walker, L. L. Conte, P. Koehl, M. Levitt, and S. E. Brenner. Astral compendium enhancements. Nucl. Acids. Res., 30:260-263, 2002.
P. Koehl and M. Levitt. Improved recognition of native-like protein structures using a family of designed sequences. Proc. Natl. Acad. Sci. (USA), 99:691-696, 2002.
P. Agarwal, L. Guibas, H. Edelsbrunner, J. Erickson, M. Isard, S. Har-Paled, J. Hershberger, C. Jensen, L. Kavraki, P. Koehl, M. Lin, D. Manocha, D. Metaxas, B. Mirtich, D. Mount, S. Muthukrishnan, D. Pai, E. Sacks, J. Snoeyink, S. Suri, and O. Wolfson. Algorithmic issues in modeling motion. ACM Computing surveys, 34:550-572, 2002.
P. Koehl. Recent progress in computational protein design. In M. Gromiha and S. Selvaraj, editors, Protein folding, stability, and design, pages 307-324. Research Signpost, Trivvendrum, India, 2002.
J. E. Wedeking, C. B. Trame, M. Dorywalska, P. Koehl, T. M. Rasche, M. McKee, D. Fitzgerald, R. J. Collier, and D. B. McKay. Refined crystallographic structure of pseudomonas aeruginosa exotoxin a and its implications for the molecular mechanism of toxicity. J. Mol. Biol., 314:823-837, 2001.
P. Rabier, B. Kieffer, P. Koehl, and J. F. Lefèvre. Fast measurements of heteronuclear relaxation: frequency domain analysis of NMR accordion spectroscopy. Mag. Res. Chem., 39:447-456, 2001.
P. Koehl and M. Levitt. De novo protein design. In O. Jardetzky and M. D. Finucane, editors, NATO ASI Series vol. 315, pages 57-75. Plenum press, New York, NY, 2001.
P. Koehl. Protein structure similarities. Curr. Opin. Struct. Biol., 11:348-353, 2001.
R. Samudrala, E. S. Huang, P. Koehl, and M. Levitt. Constructing side-chains on near native main chains for ab initio protein structure prediction. Prot. Eng., 13:453-457, 2000.
S. E. Brenner, P. Koehl, and M. Levitt. The Astral compendium for protein structure and sequence analysis. Nucl. Acids. Res., 28:254-256, 2000.
P. Koehl and M. Levitt. De novo protein design. I. in search of stability and specificity. J. Mol. Biol., 293:1161-1181, 1999.
P. Koehl and M. Levitt. De novo protein design. II. plasticity of protein sequences.
J. Mol. Biol., 293:1182-1193, 1999.
P. Koehl and M. Levitt. Structure-based conformational preferences of amino acids. Proc. Natl. Acad. Sci. (USA), 96:12524-12529, 1999.
P. Koehl. Linear prediction spectral analysis of NMR data. Progress in NMR spectroscopy, 34:257-299, 1999.
P. Koehl and M. Levitt. A brighter future for protein structure prediction. Nature Struct. Biol., 6:108-111, 1999.
P. Koehl and M. Levitt. Theory and simulation: Can theory challenge experiment? Curr. Opin. Struct. Biol., 9:155-156, 1999.
E. S. Huang, P. Koehl, M. Levitt, R. V. Pappu, and J. W. Ponder. Accuracy of side-chain prediction upon near-native protein backbones generated by ab-initio folding methods. Proteins: Struct. Func. Genet., 33:204-217, 1998.
E. Furuichi and P. Koehl. Influence of protein structure database on the predictive power of statistical pair potentials. Proteins: Struct. Func. Genet., 31:139-149, 1998.
P. Koehl and M. Delarue. Building protein lattice models using self consistent mean field theory. J. Chem. Phys., 108:9540-9549, 1998.
P. Koehl and M. Delarue. The native sequence determines sidechain packing in a protein, but does optimal sidechain packing determine the native sequence? In Proc. Pacific Symp. Biocomputing, pages 198-209, 1997.
M. Delarue and P. Koehl. The inverse protein folding problem: self consistent mean field optimization of a structure specific mutation matrix. In Proc. Pacific Symp. Biocomputing, pages 109-121, 1997.
S. Sunada, N. Go, and P. Koehl. Calculation of NMR order parameters in proteins by normal mode analysis. J. Chem. Phys., 104:4768-4775, 1996.
P. Koehl and M. Delarue. Mean field minimization methods for biological macromolecules. Curr. Opin. Struct. Biol., 2:222-226, 1996.
P. Koehl, C. Ling, and J. F. Lefèvre. Automatic phase correction of NMR spectra: statistics and limits. J. Chim. Phys., 92:1929-1938, 1995.
M. Delarue and P. Koehl. Atomic environment energies in proteins defined from statistics of accessible and contact surface areas. J. Mol. Biol., 249:675-690, 1995.
P. Koehl and M. Delarue. A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modeling. Nature Struct. Biol., 2:163-170, 1995.
P. Koehl and J. F. Lefèvre. Relaxation matrix refinement: Nucleic acids. In D. M. Grant and R. K. Harris, editors, Encyclopedia of Nuclear Magnetic Resonance. Wiley, Chichester, England, 1995.
P. Koehl and M. Delarue. Modeling side-chain conformation in proteins: a self consistent mean field approach. In M. Geisow and R. Epton, editors, Protein Engineering and Complementary Technologies, pages 31-34. Mayflower Worldwide Ltd, Birmingham, England, 1995.
G. Mer, C. Kellenberger, P. Koehl, R. Stote, O. Sorokine, A. Van Dorsselaer, B. Luu, H. Hietter, and J. F. Lefèvre. Disulphide bridge pairing and solution structure by 1H NMR of PMPD2, a 35 residue peptide isolated from Locusta migratoria. Biochemistry, 33:15397-15409, 1994.
P. Koehl and M. Delarue. Polar and non-polar atomic environments in the protein core: implications for folding and binding. Proteins: Struct. Func. Genet., 20:264-278, 1994.
P. Koehl, C. Ling, and J. F. Lefèvre. Oversampling improves linear prediction quantification of magnetic resonance spectral parameters. J. Chim. Phys., 91:595-606, 1994.
P. Koehl and M. Delarue. Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy. J. Mol. Biol., 239:249-275, 1994.
P. Koehl, C. Ling, and J. F. Lefèvre. Linear prediction quantification of magnetic resonance spectral parameters: statistics and limits. J. Magn. Reson., A109:32-40, 1994.
G. Mohn, P. Koehl, H. Budzikiewicz, and J. F. Lefèvre. Solution structure of pyoverdin GM-II. Biochemistry, 33:2843-2851, 1994.
B. Bersch, P. Koehl, Y. Nakatani, G. Ourisson, and A. Milon. 1H nuclear magnetic resonance determination of the membrane-bound conformation of senktide, a highly selective neurokinin B agonist. J. Biol. NMR, 3:91-112, 1993.
B. Kieffer, P. Koehl, S. Plaue, and J. F. Lefèvre. Structural and dynamic studies of two antigenic loops from haemagglutinin: a relaxation matrix approach. J. Biol. NMR, 3:91-112, 1993.
B. Kieffer, P. Koehl, and J. F. Lefèvre. Modeling the dynamic of an antigenic peptide using NMR data. Biochimie, 74:815-824, 1992.
P. Koehl, B. Kieffer, and J. F. Lefèvre. Computer-assisted assignment of biological macromolecule NMR spectra. J. Chim. Phys., 89:135-146, 1992.
P. Koehl, J. F. Lefèvre, and O. Jardetzky. Computing the geometry of a molecule in dihedral angle space using NMR-derived constraints: a new algorithm based on optimal filtering.J. Mol. Biol., 223:299-315, 1992.
P. Koehl, D. Burnouf, and R. P. P. Fuchs. Mutagenesis induced by a single acetylaminofluorene adduct within the nari site is position dependent. In P. C. Howard, S. S. Hecht, and F. A. Beland, editors, Nitroarenes: Occurrence, Metabolism and Biological Impact, pages 105-112. Plenum Press, New York, NY, 1991.
P. Koehl and J. F. Lefèvre. The relaxation matrix reconstructed from an incomplete set of 2D-NOE data: Statistics and limits. Bull. Magn. Reson., 12:23-29, 1990.
P. Koehl and J. F. Lefèvre. The reconstruction of the relaxation matrix from an incomplete set of nuclear Overhauser effects. J. Magn. Reson., 87:565-583, 1990.
P. Koehl, B. Kieffer, and J. F. Lefèvre. The dynamics of oligonucleotides and peptides determined by proton NMR. In O. Jardetzky, editor, NATO ASI Series vol. 183, pages 139-154. Plenum press, New York, NY, 1990.
D. Burnouf, P. Koehl, and R. P. P. Fuchs. Position of a single acetylaminofluorene adduct within a mutational hot spot is critical for the related mutagenic event. In Y. Kuroda, D. M. Shankel, and M. D. Waters, editors, Antimutagenesis and Anticarcinogenesis Mechanisms II, pages 277-288. Plenum Press, New York, NY, 1990.
P. Koehl, P. Valladier, J. F. Lefèvre, and R. P. P. Fuchs. Strong structural effect of the position of a single acetylaminofluorene adduct within a mutation hot spot. Nucl. Acids. Res., 17:9531-9541, 1989.
D. Burnouf, P. Koehl, and R. P. P. Fuchs. Single adduct mutagenesis : Strong effect of the position of a single acetylaminofluorene adduct within a mutation hot spot. Proc. Natl. Acad. Sci. (USA), 86:4147-4151, 1989.
P. Koehl, D. Burnouf, and R. P. P. Fuchs. Construction of plasmids containing a unique acetylaminofluorene adduct located within a mutation hot spot: A new probe for frameshift mutagenesis. J. Mol. Biol., 207:355-364, 1989.
A. Chatterjee, P. Koehl, and J. L. Magee. Theoretical consideration of the chemical pathways for radiation-induced strand breaks. Adv. Space Res., 6:97-105, 1986.