2012-2011

• E. DiLuccio and P. Koehl. The H-factor as a novel quality metric for homology modeling. J. of Clin. Bioinfo., 2, 18-26 (2012).
• E. Kang and P. Koehl. Identifying alpha-helices in proteins using the contact map and morphological operations. Journal of Korean Institute of Next Generation Computing (in Korean), 8, 75-86 (2012).
• P. Mach and P. Koehl. An analytical method for computing atomic contact areas in biomolecules, J. Comp. Chem., in press (2012).
• P. Koehl, Fast Recursive Computation of 3D Geometric Moments from Surface Meshes,IEEE Transactions on Pattern Analysis and Machine Intelligence, 09 Jan. 2012. IEEE computer Society Digital Library. IEEE Computer Society (2012).
• 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 letters , 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, Compuater Aided Geometric 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).

2010-2009

• 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: Structure, Function and Bioinformatics, 78, 1736-1747 (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. Lett.,102, 087801 (2009).
• X. Shi and P. Koehl. Adaptive surface meshes coarsening with guaranteed quality and topology. In ``Proceedings of the 2009 Computer Graphics International Conference'', editor S. Spence, pp 53-61 (2009).
• Laowanapiban, P, Kapustina, M., Vonrhein, C., Delarue, M., Koehl, P, Carter, CW 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).

2008-2007

• C. Azuara, M. Bon, H. Orland, P. Koehl and M. Delarue. Incorporating dipolar solvents with variable density in biomolecular electrostatics: the Poisson-Boltzmann-Langevin view. Biophys. J. (in press) (2008).
  
• V. Natarajan, P. Koehl, Y. Wang and B. Hamann. Visual analysis of biomolecular surfaces, in: Linsen, L., Hagen, H. and Hamann, B., eds., Visualization in Medicine and Life Sciences, Springer-Verlag, Heidelberg, Germany, pp. 237-255 (2008). pdf_file
• X. Shi and P. Koehl. The geometry behind numerical solvers of the Poisson-Boltzmann equation. Commun. Comput. Phys., 3, 1032-1050 (2008). pdf_file
• 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. Nucleic Acids Res. 35 W477-W482 (2007). pdf_file
• 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 Molecular Biology, 8, 74-85 (2007).
• S. Gu, O. Poch, B. Hamann and P. Koehl. A geometric representation of protein sequences. IEEE International Conference on Biology and Medicine, 2007. BIBM, 135-142 (2007). pdf_file

2006-2005

• P. Koehl. Electrostatics calculations: latest methodological advances.. Curr. Opin. Struct. Biol., 16, 142-151 (2006). pdf_file
• P. Koehl. Protein structure classification. Reviews Comput. Chem., 22, 1-56 (2006). pdf_file
• C. Azuara, E. Lindahl, P. Koehl, H. Orland and M. Delarue. PDB_HYDRO: incorporating dipolar solvents with variable dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics. Nucleic Acids. Res. 34: W38-W42 (2006). pdf_file
• E. Lindahl, C. Azuara, P. Koehl and M. Delarue. NORMANDREF: Visualisation deformation and refinement of macromolecular structures based on all-atom normal mode analysis. Nucleic. Acids. Res. 34: W52-W56 (2006). pdf_file
• A. Zomorodian, L. Guibas and P. Koehl. Geometric filtering of pairwaise atomic interactions applied to the design of efficient statistical potentials. Comput. Aided. Graph. Des. 23: 531-544 (2006). pdf_file
• L. McHale, X. Tan, P. Koehl and R. Michelmore. Plant NBS-LRR proteins: adaptable guards.. Genome Biology. (published online April 26 2006).pdf_file
• 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. Nucleic Acids Res., 33, (2005). pdf_file
• J.D. Thompson, P. Koehl, R. Ripp and O. Poch. BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark. Proteins: Struct. Func. Bioinfo. , 61, (2005). pdf_file
• H. Edelsbrunner and P. Koehl. The geometry of biomolecular solvation. Combinatorial and Computational Geometry (MSRI Publications) 52, 243-275 (2005). pdf_file
• P. Koehl. Relaxed specificity in aromatic prenyltransferases. Nature Chem. Biol., 1, 71-72 (2005). pdf_file
• R. Kolodny, L. Guibas, M. Levitt and P. Koehl. Inverse kinematics in biology: the protein loop closure problem. International J. Robotics. Research, 24, 151-163 (2005). pdf_file
• 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). pdf_file

2004-2003

• C. Birck, L. Damian, C. Marty-Detraves, A. Lougarre, C. Schulze Briese, P. Koehl, D. Fournier, 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. 344, 1409-1420 (2004). pdf-file
• J.M. Chandonia, N.S. Walker, L.L. Conte, P. Koehl, M. Levitt and S.E. Brenner. Astral compendium enhancements, Nucleic Acids Res., 32, D189-D192 (2004). pdf-file
• 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). pdf_file
• H. Edelsbrunner and P. Koehl. The weighted volume derivative of a space filling diagram. Proc. Natl. Acad. Sci. (USA) 100, 2203-2208 (2003). pdf-file

2002-2001

• P. Koehl and M. Levitt. Sequence variations within protein families are linearly related to structural variations, J. Mol. Biol., 323, 551-562 (2002). pdf-file
• P. Koehl and M. Levitt. Protein topology and Stability define the space of allowed sequences, Proc. Natl. Acad. Sci. (USA), 99, 1280-1285 (2002). pdf-file
• P. Koehl and M. Levitt. Improved recognition of native-like protein structures using a family of designed sequences, Proc. Nat. Acad. Sci. (USA), 99, 691-696 (2002). pdf-file
• P. Koehl. Recent progress in Computational Protein Design. in Protein Folding, Stability and Design, 307-323 (eds M. Gromiha and S. Selvaraj), Research Signpost, Tiruchirapalli, India (2002).
• J.M. Chandonia, N.S. Walker, L.L. Conte, P. Koehl, M. Levitt and S.E. Brenner. Astral compendium enhancements, Nucleic Acids Res., 30, 260-263 (2002). pdf-file
• P. Aggarwal, L.J. Guibas, H. Edelsbrunner, J. Erikson, M. Isard, S. Har-Peled, 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, O. Wolfson. Algorithmic issues in modeling motions. ACM computing surveys, 34, 550-572 (2002). pdf_file
• 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). pdf-file
• P. Koehl and M. Levitt. De novo Protein Design. in Dynamics, Structure and Function of Biological Macromolecules, 57-75 (eds O. Jardetzky and M.D. Finucane), IOS Press, Amsterdam (2001).
• P. Koehl. Protein Structure Similarities, Curr. Opin. Struct. Biol. 11, 348-353 (2001). pdf_file
• J.E. Wedeking, C.B. Trame, M. Dorywalska, P. Koehl, T.M. Raschke, 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). pdf-file
• P. Rabier, B. Kieffer, P. Koehl and JF Lefevre. "Fast measurements of heteronuclear relaxation: frequency domain analysis of NMR accordion spectroscopy", Mag Res Chem 39, 447-456 (2001). pdf-file

2000-1999

• S.E. Brenner, P. Koehl and M. Levitt, The Astral compendium for protein structure and sequence analysis, Nucleic Acids Res., 28, 254-256 (2000). pdf-file
• 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). pdf-file
• P. Koehl and M. Levitt, De novo protein design. I. In search of stability and specificity, J. Mol. Biol., 293, 1161-1181 (1999). pdf-file
• P. Koehl and M. Levitt, De novo protein design. II. Plasticity of protein sequence, J. Mol. Biol., 293, 1183-1193 (1999). pdf-file
• P. Koehl and M. Levitt, Structure-based conformational preferences of amino acids, Proc. Nat. Acad. Sci. (USA), 96, 12524-12529 (1999). pdf_file
• P. Koehl and M. Levitt. A brighter future for protein structure prediction. Nature Struct. Biol. 6, 108-111 (1999). pdf-file
• P. Koehl and M. Levitt. Theory and simulation: Can theory challenge experiment?, Curr. Opin. Struct. Biol. 9, 155-156 (1999). pdf_file
• P. Koehl Linear prediction spectral analysis of NMR data, Progress in NMR spectroscopy. 34, 257-299 (1999) pdf_file

1998-1997

• 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. Funct. Genet., 33, 204-217 (1998). pdf-file
• E. Furuichi and P. Koehl. Influence of protein structure database on the predictive power of statistical pair potentials, Proteins: Struct. Funct. Genet., 31, 139-149 (1998). pdf-file
• P. Koehl and M. Delarue. Building protein lattice models using self consistent mean field theory, J. Chem. Phys., 108, 9540-9549 (1998). pdf-file
• P. Koehl and M. Delarue, The native sequence determines sidechain packing in a protein, but does optimal sidechain packing determine the native sequence?, in Proceedings of the Pacific Symposium on Biocomputing, 1997, 198-209 (eds. R.B. Altman, A.K. Dunker, L. Hunter and T. Klein), World Scientific, Singapore (1997).
• M. Delarue and P. Koehl, The inverse protein folding problem: self consistent mean field optimization of a structure specific mutation matrix, in Proceedings of the Pacific Symposium on Biocomputing, 1997, 109-121 (eds. R.B. Altman, A.K. Dunker, L. Hunter and T. Klein), World Scientific, Singapore (1997).

1996 and before

• P. Koehl and M. Delarue, Mean field minimization methods for biological macromolecules, Curr. Opin. Struct. Biol. 2, 222-226 (1996). pdf_file
• 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). pdf-file
• P. Koehl and J.F. Lefèvre, Relaxation Matrix Refinement: Nucleic Acids, in Encyclopedia of Nuclear Magnetic Resonance (eds D.M. Grant and R.K. Harris), John Wiley, Chichester, England (1995).
• P. Koehl and M. Delarue, Modeling side-chain conformation in proteins: a self consistent mean field approach in Protein Engineering and Complementary Technologies (eds M. Geisow and R. Epton), Mayflower Worldwide Ltd., Birmingham, England, 31-34 (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).
• 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). pdf_file
• P. Koehl and M. Delarue. Polar and non-polar atomic environments in the protein core: implications for folding and binding Protein: Struct. Funct. Genet., 20, 264-278 (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). pdf_file
• 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). pdf_file
• G. Mohn, P. Koehl, H. Budzikiewicz and J.F. Lefèvre Solution structure of pyoverdin GM-II, Biochemistry, 33, 2843-2851 (1994). pdf_file
• 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. 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, 443-461 (1993).
• P. Koehl, B. Kieffer and J.F. Lefèvre, Computer-assisted assignment of biological macromolecule NMR spectra, J. Chim. Phys., 89, 135-146 (1992).
• 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, 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 Nitroarenes: Occurrence, Metabolism and Biological Impact, (eds P.C. Howard, S.S. Hecht and F.A. Beland), Plenum Press, New York, 105-112 (1991).
• P. Koehl, B. Kieffer and J.F. Lefèvre, The dynamics of oligonucleotides and peptides determined by proton NMR, in Protein Structure and Engineering, (editor O. Jardetzky), NATO ASI series, 183, 139-154 (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 and J.F. Lefèvre, The relaxation matrix reconstructed from an incomplete set of 2D-NOE data: Statistics and Limits, Bull. Magn. Reson., 12 1/2, 23-29 (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 Antimutagenesis and Anticarcinogenesis Mechanisms II, (eds Y. Kuroda, D.M. Shankel and M.D. Waters) Plenum Press, New York, 277-288 (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, Nucleic Acids Res., 17, 9531-9541 (1989). pdf_file
• 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. Nat. Acad. Sci. (USA), 86, 4147-4151 (1989). pdf_file
• 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).