P. Koehl

发表

Protein structure similarities.

P. Koehl, Patrice Koehl, 2001, Current opinion in structural biology.

Accuracy of side‐chain prediction upon near‐native protein backbones generated by ab initio folding methods

M. Levitt, P. Koehl, E. Huang, 1998, Proteins.

Ab initio sampling of transition paths by conditioned Langevin dynamics.

P. Koehl, H. Orland, M. Delarue, 2017, The Journal of chemical physics.

Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures.

Rachel Kolodny, Patrice Koehl, Michael Levitt, 2005, Journal of molecular biology.

Geometric filtering of pairwise atomic interactions applied to the design of efficient statistical potentials

Leonidas J. Guibas, Afra Zomorodian, Patrice Koehl, 2006, Comput. Aided Geom. Des..

Polar and nonpolar atomic environments in the protein core: Implications for folding and binding

P. Koehl, M. Delarue, 1994, Proteins.

Influence of protein structure databases on the predictive power of statistical pair potentials

P. Koehl, E. Furuichi, 1998, Proteins.

Atomic environment energies in proteins defined from statistics of accessible and contact surface areas.

P. Koehl, M. Delarue, 1995, Journal of molecular biology.

Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy.

P. Koehl, M. Delarue, Patrice Koehl, 1994, Journal of molecular biology.

The ASTRAL Compendium in 2004

Patrice Koehl, Steven E. Brenner, Michael Levitt, 2003, Nucleic Acids Res..

Comparative Normal Mode Analysis of the Dynamics of DENV and ZIKV Capsids

P. Koehl, M. Delarue, Y.-C. Hsieh, 2016, Front. Mol. Biosci..

Electrostatics calculations: latest methodological advances.

P. Koehl, 2006, Current opinion in structural biology.

A METRIC FOR GENUS-ZERO SURFACES

P. Koehl, J. Hass, 2015, 1507.00798.

Landmark-free geometric methods in biological shape analysis

P. Koehl, J. Hass, 2015, Journal of The Royal Society Interface.

Computing the geometry of a molecule in dihedral angle space using n.m.r.-derived constraints. A new algorithm based on optimal filtering.

O Jardetzky, P. Koehl, O. Jardetzky, 1992, Journal of molecular biology.

Small libraries of protein fragments model native protein structures accurately.

M. Levitt, R. Kolodny, P. Koehl, 2002, Journal of molecular biology.

Plant NBS-LRR proteins: adaptable guards

Patrice Koehl, P. Koehl, R. Michelmore, 2006, Genome Biology.

65 COMPUTATIONAL TOPOLOGY FOR STRUCTURAL MOLECULAR BIOLOGY

P. Koehl, H. Edelsbrunner, 2017 .

Multi-Scale Clustering by Building a Robust and Self Correcting Ultrametric Topology on Data Points

P. Koehl, H. Fushing, B. McCowan, 2013, PloS one.

Improved recognition of native-like protein structures using a family of designed sequences

M. Levitt, P. Koehl, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Electrostatics, proton sensor, and networks governing the gating transition in GLIC, a proton-gated pentameric ion channel

P. Koehl, M. Delarue, P. Corringer, 2018, Proceedings of the National Academy of Sciences.

Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels

P. Koehl, M. Delarue, M. Baaden, 2013, The EMBO journal.

A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modelling

P. Koehl, M. Delarue, 1995, Nature Structural Biology.

LINEAR PREDICTION SPECTRAL ANALYSIS OF NMR DATA

P. Koehl, 1999 .

ASTRAL compendium enhancements

Patrice Koehl, Steven E. Brenner, Michael Levitt, 2002, Nucleic Acids Res..

Protein Structure Classification

Patrice Koehl, P. Koehl, 2006 .

representations of amino acids — applications to protein sequence comparison and classi fi cation

P. Koehl, Jie Li, 2014 .

Capturing protein sequence–structure specificity using computational sequence design

P. Koehl, Paul Mach, 2013, Proteins.

Protein Structure Prediction

Patrice Koehl, P. Koehl, 2010 .

Sequence variations within protein families are linearly related to structural variations.

Patrice Koehl, Michael Levitt, M. Levitt, 2002, Journal of molecular biology.

Solvation of Ion Pairs: The Poisson-Langevin Model

P. Koehl, H. Orland, M. Delarue, 2009, 2009 International Conference on Signal Processing Systems.

Protein topology and stability define the space of allowed sequences

Patrice Koehl, Michael Levitt, M. Levitt, 2002, Proceedings of the National Academy of Sciences of the United States of America.

MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences

Patrice Koehl, Olivier Poch, Stephen R. Holbrook, 2005, Nucleic acids research.

Statistical Physics Approach to the Optimal Transport Problem.

P. Koehl, H. Orland, M. Delarue, 2019, Physical review letters.

Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations

P. Koehl, M. Delarue, C. Carter, 2009, Proceedings of the National Academy of Sciences.

PackHelix: A tool for helix‐sheet packing during protein structure prediction

P. Koehl, N. Max, Chengcheng Hu, 2011, Proteins.

Helix‐sheet packing in proteins

P. Koehl, Chengcheng Hu, 2010, Proteins.

Extracting knowledge from protein structure geometry

P. Koehl, P. Røgen, 2013, Proteins.

Incorporating dipolar solvents with variable density in Poisson-Boltzmann electrostatics.

Patrice Koehl, Marc Delarue, Henri Orland, 2008, Biophysical journal.

Combined approaches from physics , statistics , and computer science for protein structure prediction : ab initio ex unitate vires ( unity is strength ) ?

P. Koehl, M. Delarue, 2019 .

The geometry of colors in van Gogh’s Sunflowers

P. Koehl, F. Hsieh, Shuting Liao, 2021, Heritage Science.

A new lectin family with structure similarity to actinoporins revealed by the crystal structure of Xerocomus chrysenteron lectin XCL.

P. Koehl, C. Schulze-Briese, C. Birck, 2004, Journal of molecular biology.

Minimum action principle and shape dynamics

P. Koehl, 2017, Journal of The Royal Society Interface.

Computing ion solvation free energies using the dipolar Poisson model.

P. Koehl, H. Orland, M. Delarue, 2009, The journal of physical chemistry. B.

Modified Poisson–Boltzmann equations for characterizing biomolecular solvation

P. Koehl, H. Orland, M. Delarue, 2014 .

On the Importance of the Distance Measures Used to Train and Test Knowledge-Based Potentials for Proteins

P. Koehl, P. Røgen, Martin Carlsen, 2014, PloS one.

Coarse-grained dynamics of supramolecules: Conformational changes in outer shells of Dengue viruses.

P. Koehl, M. Delarue, 2019, Progress in biophysics and molecular biology.

Adapting Poisson-Boltzmann to the self-consistent mean field theory: application to protein side-chain modeling.

P. Koehl, H. Orland, M. Delarue, 2011, The Journal of chemical physics.

Rod-derived Cone Viability Factor-2 is a novel bifunctional-thioredoxin-like protein with therapeutic potential

P. Koehl, T. Léveillard, J. Sahel, 2007, BMC Molecular Biology.

Sampling constrained stochastic trajectories using Brownian bridges

P. Koehl, H. Orland, 2022, The Journal of Chemical Physics.

Numerical Encodings of Amino Acids in Multivariate Gaussian Modeling of Protein Multiple Sequence Alignments

P. Koehl, H. Orland, M. Delarue, 2018, Molecules.

Sampling constrained stochastic trajectories using Brownian bridges.

P. Koehl, H. Orland, 2022, The Journal of chemical physics.

The geometry of colors in van Gogh’s Sunflowers

P. Koehl, F. Hsieh, Shuting Liao, 2021, Heritage Science.

Geometric Potentials for Computational Protein Sequence Design.

P. Koehl, Jie Li, 2017, Methods in molecular biology.

Solution structure of PMP-D2, a 35-residue peptide isolated from the insect Locusta migratoria.

P. Koehl, J. Lefèvre, R. Stote, 1994, Biochemistry.

Relaxed specificity in aromatic prenyltransferases

P. Koehl, 2005, Nature chemical biology.

TheGeometry BehindNumerical Solvers of the Poisson Boltzmann Equation

P. Koehl, Xinwei Shi, 2007 .

Bootstrapping on Undirected Binary Networks Via Statistical Mechanics

P. Koehl, H. Fushing, Shan-Yu Liu, 2014, Journal of Statistical Physics.

String kernels for protein sequence comparisons: improved fold recognition

P. Koehl, Saghi Nojoomi, 2017, BMC Bioinformatics.

A programme for the inventory, characterisation, evaluation, conservation and utilisation of European rabbit (Oryctolagus cuniculus) genetic resources

P. Koehl, N. Ferrand, M. Durand-Tardif, 1999 .

Comparing shapes of genus-zero surfaces

Patrice Koehl, Joel Hass, P. Koehl, 2017, J. Appl. Comput. Topol..

Linear Prediction Spectral Analysis of NMR Data

Patrice Koehl, P. Koehl, 1999 .

Geometric measures of large biomolecules: Surface, volume, and pockets

Patrice Koehl, Paul Mach, P. Koehl, 2011, J. Comput. Chem..

The geometry of biomolecular solvation

Herbert Edelsbrunner, Patrice Koehl, P. Koehl, 2005 .

De novo protein design. II. Plasticity in sequence space.

M. Levitt, P. Koehl, 1999, Journal of molecular biology.

De novo protein design. I. In search of stability and specificity.

M. Levitt, P. Koehl, 1999, Journal of molecular biology.

Surface‐histogram: A new shape descriptor for protein‐protein docking

Nina Amenta, Patrice Koehl, Joel Hass, 2012, Proteins.

DCG++: A data-driven metric for geometric pattern recognition

Patrice Koehl, Fushing Hsieh, Jiahui Guan, 2019, PloS one.

Unravelling the geometry of data matrices: effects of water stress regimes on winemaking

Patrice Koehl, Hsieh Fushing, Chih-Hsin Hsueh, 2015, Journal of The Royal Society Interface.

Bootstrapping on Undirected Binary Networks Via Statistical Mechanics

Chen Chen, Patrice Koehl, Hsieh Fushing, 2014, Journal of Statistical Physics.

Faculty Opinions recommendation of OpenMM 7: Rapid development of high performance algorithms for molecular dynamics.

Patrice Koehl, P. Koehl, 2018, Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature.

Fast computation of exact solutions of generic and degenerate assignment problems.

Patrice Koehl, Henri Orland, P. Koehl, 2021, Physical review. E.

Optimal transport at finite temperature.

Patrice Koehl, Marc Delarue, Henri Orland, 2019, Physical review. E.

The reconstruction of the relaxation matrix from an incomplete set of nuclear overhauser effects

P. Koehl, J. Lefèvre, 1990 .

The native sequence determines sidechain packing in a protein, but does optimal sidechain packing determine the native sequence?

P. Koehl, M. Delarue, 1997, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

Computational Topology for Structural Molecular Biology

Herbert Edelsbrunner, Patrice Koehl, P. Koehl, 2017 .

The ASTRAL compendium for protein structure and sequence analysis

Patrice Koehl, Steven E. Brenner, Michael Levitt, 2000, Nucleic Acids Res..

Computational assembly of polymorphic amyloid fibrils reveals stable aggregates.

Patrice Koehl, Jérôme Waldispühl, Frédéric Poitevin, 2013, Biophysical journal.

Position of a single acetylaminofluorene adduct within a mutational hot spot is critical for the related mutagenic event.

P. Koehl, R. Fuchs, D. Burnouf, 1990, Basic life sciences.

Combined approaches from physics, statistics, and computer science for ab initio protein structure prediction: ex unitate vires (unity is strength)?

Patrice Koehl, Marc Delarue, P. Koehl, 2018, F1000Research.

Structure-based conformational preferences of amino acids.

M. Levitt, P. Koehl, 1999, Proceedings of the National Academy of Sciences of the United States of America.

Single adduct mutagenesis: strong effect of the position of a single acetylaminofluorene adduct within a mutation hot spot.

P. Koehl, R. Fuchs, D. Burnouf, 1989, Proceedings of the National Academy of Sciences of the United States of America.

Relaxation Matrix Refinement of Nucleic Acids

P. Koehl, J. Lefèvre, 2007 .

Calculation of nuclear magnetic resonance order parameters in proteins by normal mode analysis

Patrice Koehl, Nobuhiro Go, P. Koehl, 1996 .

Structural and dynamic studies of two antigenic loops from haemagglutinin: A relaxation matrix approach

P. Koehl, J. Lefèvre, B. Kieffer, 1993, Journal of biomolecular NMR.

Modelling the dynamics of an antigenic peptide using NMR relaxation data.

P. Koehl, J. Lefèvre, B. Kieffer, 1992, Biochimie.

The Dynamics of Oligonucleotides and Peptides Determined by Proton NMR

P. Koehl, J. Lefèvre, B. Kieffer, 1989 .

Beyond the Poisson-Boltzmann model: modeling biomolecule-water and water-water interactions.

Patrice Koehl, Marc Delarue, Henri Orland, 2009, Physical review letters.

The weighted-volume derivative of a space-filling diagram

Herbert Edelsbrunner, Patrice Koehl, P. Koehl, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Physics approach to the variable-mass optimal-transport problem.

P. Koehl, H. Orland, M. Delarue, 2021, Physical review. E.

Identifying essential pairwise interactions in elastic network model using the alpha shape theory

Steven C. H. Hoi, Fei Xia, Dudu Tong, 2014, J. Comput. Chem..

Protein side‐chain modeling with a protein‐dependent optimized rotamer library

Patrice Koehl, Patricia Francis-Lyon, P. Koehl, 2014, Proteins.

How round is a protein? Exploring protein structures for globularity using conformal mapping

Patrice Koehl, Joel Hass, P. Koehl, 2014, Front. Mol. Biosci..

Mathematics's role in the grand challenge of deciphering the molecular basis of life

Patrice Koehl, P. Koehl, 2014, Front. Mol. Biosci..

Parameterizing elastic network models to capture the dynamics of proteins

Patrice Koehl, Marc Delarue, Henri Orland, 2021, J. Comput. Chem..

BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark

Olivier Poch, Patrice Koehl, Raymond Ripp, 2005, Proteins.

Constructing side chains on near-native main chains for ab initio protein structure prediction.

R Samudrala, M Levitt, E S Huang, 2000, Protein engineering.

1H nuclear magnetic resonance determination of the membrane-bound conformation of senktide, a highly selective neurokinin B agonist

P. Koehl, G. Ourisson, A. Milon, 1993, Journal of biomolecular NMR.

Mutagenesis Induced by a Single Acetylaminofluorene Adduct Within the NarI Site is Position Dependent

P. Koehl, R. Fuchs, D. Burnouf, 1990 .

Construction of plasmids containing a unique acetylaminofluorene adduct located within a mutation hot spot. A new probe for frameshift mutagenesis.

P. Koehl, R. Fuchs, D. Burnouf, 1989, Journal of molecular biology.

Strong structural effect of the position of a single acetylaminofluorene adduct within a mutation hot spot.

P. Koehl, J. Lefèvre, R. Fuchs, 1989, Nucleic acids research.

Structural alphabets for protein structure classification: a comparison study.

Gianluca Pollastri, Patrice Koehl, Quan Le, 2009, Journal of molecular biology.

NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis

Patrice Koehl, Erik Lindahl, Marc Delarue, 2006, Nucleic Acids Res..

Solution structure of pyoverdin GM-II.

P. Koehl, J. Lefèvre, H. Budzikiewicz, 1994, Biochemistry.

Extracting information from RNA SHAPE data: Kalman filtering approach

Patrice Koehl, Sharon Aviran, Sana Vaziri, 2018, bioRxiv.

The Renormalization Group and Its Applications to Generating Coarse-Grained Models of Large Biological Molecular Systems.

Patrice Koehl, Frédéric Poitevin, Rafael Navaza, 2017, Journal of chemical theory and computation.

His74 conservation in the bilin reductase PcyA family reflects an important role in protein-substrate structure and dynamics.

P. Koehl, A. Fisher, J. Lagarias, 2013, Archives of biochemistry and biophysics.

AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models

Sebastian Doniach, Patrice Koehl, Marc Delarue, 2011, Nucleic Acids Res..

Methods for Global Organization of All Known Protein Sequences It Was a Pleasure to Work with the Great Team of Students with Whom I Created the Protomap Web Site. I Thank

Shlomo Dubnov, Golan Yona, Yoav Etsion, 1999 .

Morphing methods to visualize coarse-grained protein dynamics.

Patrice Koehl, Dahlia R. Weiss, Dahlia R Weiss, 2014, Methods in molecular biology.

Algorithmic issues in modeling motion

Leonidas J. Guibas, Dinesh Manocha, Christian S. Jensen, 2002, CSUR.

Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives

P. Koehl, H. Edelsbrunner, A. Akopyan, 2023, J. Chem. Inf. Model..

MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape

Sebastian Doniach, Patrice Koehl, Marc Delarue, 2007, Nucleic Acids Res..

Measuring the shapes of macromolecules – and why it matters

Jie Li, Patrice Koehl, Paul Mach, 2013, Computational and structural biotechnology journal.

Refined crystallographic structure of Pseudomonas aeruginosa exotoxin A and its implications for the molecular mechanism of toxicity.

P. Koehl, M. Dorywalska, J. Wedekind, 2001, Journal of molecular biology.

3D representations of amino acids—applications to protein sequence comparison and classification

Jie Li, Patrice Koehl, P. Koehl, 2014, Computational and structural biotechnology journal.

biDCG: A New Method for Discovering Global Features of DNA Microarray Data via an Iterative Re-Clustering Procedure

Patrice Koehl, Hsieh Fushing, Rob Atwill, 2014, PloS one.

Minimum action transition paths connecting minima on an energy surface.

P. Koehl, 2016, The Journal of chemical physics.

Adaptive skin meshes coarsening for biomolecular simulation

Patrice Koehl, Xinwei Shi, P. Koehl, 2011, Comput. Aided Geom. Des..

AQUASOL: An efficient solver for the dipolar Poisson-Boltzmann-Langevin equation.

Patrice Koehl, Marc Delarue, P. Koehl, 2010, The Journal of chemical physics.

PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson–Boltzmann treatment of macromolecule electrostatics

Patrice Koehl, Erik Lindahl, Marc Delarue, 2006, Nucleic Acids Res..

Analyzing the Geometry and Dynamics of Viral Structures: A Review of Computational Approaches Based on Alpha Shape Theory, Normal Mode Analysis, and Poisson–Boltzmann Theories

P. Koehl, H. Orland, M. Delarue, 2023, Viruses.

A quality metric for homology modeling: the H-factor

Patrice Koehl, Eric di Luccio, P. Koehl, 2011, BMC Bioinformatics.

Inverse Kinematics in Biology: The Protein Loop Closure Problem

Leonidas J. Guibas, Patrice Koehl, Michael Levitt, 2005, Int. J. Robotics Res..

Molecular Force Fields

Patrice Koehl, P. Koehl, 2009 .

Simultaneous Identification of Multiple Binding Sites in Proteins: A Statistical Mechanics Approach.

P. Koehl, H. Orland, M. Delarue, 2021, The journal of physical chemistry. B.

Mean-field minimization methods for biological macromolecules.

P Koehl, M Delarue, P. Koehl, 1996, Current opinion in structural biology.

Barbiturates Bind in the GLIC Ion Channel Pore and Cause Inhibition by Stabilizing a Closed State*♦

P. Koehl, M. Delarue, T. Smart, 2016, The Journal of Biological Chemistry.

Sampling the conformation of protein surface residues for flexible protein docking

Nina Amenta, Patrice Koehl, Joel Hass, 2010, BMC Bioinformatics.

A Physicist's View on Partial 3D Shape Matching

P. Koehl, H. Orland, 2023, Algorithms.

Automatic Alignment of Genus-Zero Surfaces

Patrice Koehl, Joel Hass, P. Koehl, 2014, IEEE Transactions on Pattern Analysis and Machine Intelligence.

SPECTROSCOPIC AND STRUCTURAL INVESTIGATIONS ON HEXAGONAL ELPASOLITES

P. Koehl, 1977 .

Computing the Gromov-Wasserstein Distance between Two Surface Meshes Using Optimal Transport

P. Koehl, H. Orland, M. Delarue, 2023, Algorithms.

The H-factor as a novel quality metric for homology modeling

Patrice Koehl, Eric di Luccio, P. Koehl, 2012, Journal of Clinical Bioinformatics.

Faculty Opinions recommendation of Large-scale determination of previously unsolved protein structures using evolutionary information.

Patrice Koehl, P. Koehl, 2016 .

A Geometric Representation of Protein Sequences

Bernd Hamann, Patrice Koehl, Olivier Poch, 2007, 2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007).

Selective and specific ion binding on proteins at physiologically‐relevant concentrations

P. Koehl, Jianxing Song, Haina Qin, 2011, FEBS letters.

Extracting knowledge from protein structure geometry

P. Koehl, P. Røgen, 2013, Proteins.

A brighter future for protein structure prediction

Michael Levitt, Patrice Koehl, M. Levitt, 1999, Nature Structural Biology.

The Area Derivative of a Space-Filling Diagram

Herbert Edelsbrunner, Patrice Koehl, Michael Levitt, 2004, Discret. Comput. Geom..

Faculty Opinions recommendation of Constructing Markov State Models to elucidate the functional conformational changes of complex biomolecules.

Patrice Koehl, P. Koehl, 2018, Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature.

The Geometry Behind Numerical Solvers of the Poisson-Boltzmann Equation

P. Koehl, Xinwei Shi, 2008 .

Building protein lattice models using self-consistent mean field theory

Patrice Koehl, Marc Delarue, P. Koehl, 1998 .

A quality metric for homology modeling: the H-factor

P. Koehl, E. D. Luccio, 2011, BMC Bioinformatics.

Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations

P. Koehl, M. Delarue, C. Carter, 2009, Proceedings of the National Academy of Sciences.