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Statistical Physics Approach to the Optimal Transport Problem

Physical review letters, 2019-07, Vol.123 (4), p.040603-040603, Article 040603

2019

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A General Statistical Physics Framework for Assignment Problems

Algorithms, 2024-05, Vol.17 (5), p.212

2024

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A Physicist’s View on Partial 3D Shape Matching

Algorithms, 2023-07, Vol.16 (7), p.346

2023

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Stable Evaluation of 3D Zernike Moments for Surface Meshes

Algorithms, 2022-11, Vol.15 (11), p.406

2022

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Extracting information from RNA SHAPE data: Kalman filtering approach

PloS one, 2018-11, Vol.13 (11), p.e0207029-e0207029

2018

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A weighted string kernel for protein fold recognition

BMC bioinformatics, 2017-08, Vol.18 (1), p.378-378, Article 378

2017

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

PloS one, 2019-06, Vol.14 (6), p.e0217838-e0217838

2019

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Comprehensive Evaluation of Protein Structure Alignment Methods: Scoring by Geometric Measures

Journal of molecular biology, 2005-03, Vol.346 (4), p.1173-1188

2005

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

Algorithms, 2023-03, Vol.16 (3), p.131

2023

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

The EMBO journal, 2013-03, Vol.32 (5), p.728-741

2013

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BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark

Proteins, structure, function, and bioinformatics, 2005-10, Vol.61 (1), p.127-136

2005

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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

Viruses, 2023-06, Vol.15 (6), p.1366

2023

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

Molecules (Basel, Switzerland), 2019-01, Vol.24 (1), p.104

2019

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

F1000 research, 2018, Vol.7 (eCollection 2018), p.1125

2018

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On the importance of the distance measures used to train and test knowledge-based potentials for proteins

PloS one, 2014-11, Vol.9 (11), p.e109335-e109335

2014

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Capturing protein sequence-structure specificity using computational sequence design

Proteins, structure, function, and bioinformatics, 2013-09, Vol.81 (9), p.1556-1570

2013

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An analytical method for computing atomic contact areas in biomolecules

Journal of computational chemistry, 2013-01, Vol.34 (2), p.105-120

2013

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

Physical review letters, 2009-02, Vol.102 (8), p.087801-087801, Article 087801

2009

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Multi-scale clustering by building a robust and self correcting ultrametric topology on data points

PloS one, 2013-02, Vol.8 (2), p.e56259-e56259

2013

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Large Eigenvalue Problems in Coarse-Grained Dynamic Analyses of Supramolecular Systems

Journal of chemical theory and computation, 2018-07, Vol.14 (7), p.3903-3919

Koehl, Patrice

2018

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Minimum action transition paths connecting minima on an energy surface

The Journal of chemical physics, 2016-11, Vol.145 (18), p.184111-184111

Koehl, Patrice

2016

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A quality metric for homology modeling: the H-factor

BMC bioinformatics, 2011-02, Vol.12 (1), p.48-48, Article 48

2011

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The geometry of colors in van Gogh’s Sunflowers

Heritage science, 2021-10, Vol.9 (1), p.1-19, Article 136

2021

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

Computational and structural biotechnology journal, 2014-08, Vol.11 (18), p.47-58

2014

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Small Libraries of Protein Fragments Model Native Protein Structures Accurately

Journal of molecular biology, 2002-10, Vol.323 (2), p.297-307

2002

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Statistical Physics Approach to the Optimal Transport Problem

A General Statistical Physics Framework for Assignment Problems

A Physicist’s View on Partial 3D Shape Matching

Stable Evaluation of 3D Zernike Moments for Surface Meshes

Extracting information from RNA SHAPE data: Kalman filtering approach

A weighted string kernel for protein fold recognition

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

Comprehensive Evaluation of Protein Structure Alignment Methods: Scoring by Geometric Measures

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

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

BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark

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

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

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

On the importance of the distance measures used to train and test knowledge-based potentials for proteins

Capturing protein sequence-structure specificity using computational sequence design

An analytical method for computing atomic contact areas in biomolecules

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

Multi-scale clustering by building a robust and self correcting ultrametric topology on data points

Large Eigenvalue Problems in Coarse-Grained Dynamic Analyses of Supramolecular Systems

Minimum action transition paths connecting minima on an energy surface

A quality metric for homology modeling: the H-factor

The geometry of colors in van Gogh’s Sunflowers

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

Small Libraries of Protein Fragments Model Native Protein Structures Accurately

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