J. Ferkinghoff-Borg

发表

Prediction of water and metal binding sites and their affinities by using the Fold-X force field.

L. Serrano, F. Stricher, J. Schymkowitz, 2005, Proceedings of the National Academy of Sciences of the United States of America.

A generative, probabilistic model of local protein structure

Jesper Ferkinghoff-Borg, Thomas Hamelryck, Kanti V Mardia, 2008, Proceedings of the National Academy of Sciences.

Monte Carlo Methods for Inference in High-Dimensional Systems

J. Ferkinghoff-Borg, 2012 .

Kresten Lindorff-Larsen, Jesper Ferkinghoff-Borg, K. Lindorff-Larsen, 2009, PloS one.

Quantifying information transfer by protein domains: Analysis of the Fyn SH2 domain structure

L. Serrano, T. Lenaerts, F. Stricher, 2008, BMC Structural Biology.

Formulation of probabilistic models of protein structure in atomic detail using the reference ratio method

K. Mardia, Sandro Bottaro, J. Frellsen, 2014, Proteins.

Proteins, physics and probability kinematics: a Bayesian formulation of the protein folding problem

Jesper Illemann Foldager, D. Theobald, J. Frellsen, 2015 .

Potentials of Mean Force for Protein Structure Prediction Vindicated, Formalized and Generalized

Sandro Bottaro, J. Frellsen, T. Hamelryck, 2010, PloS one.

Towards a General Probabilistic Model of Protein Structure: The Reference Ratio Method

Kanti V. Mardia, Jes Frellsen, Jesper Ferkinghoff-Borg, 2012 .

Understanding of ‘Networks’ In Vitro and/or In Vivo

R. Linding, J. Ferkinghoff-Borg, E. Schoof, 2016 .

Kinome-wide Decoding of Network-Attacking Mutations Rewiring Cancer Signaling

Chad J. Miller, M. Helmer-Citterich, R. Linding, 2015, Cell.

Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts

Kresten Lindorff-Larsen, Michele Vendruscolo, Wouter Boomsma, 2014, Proceedings of the National Academy of Sciences.

Experimental parameterization of an energy function for the simulation of unfolded proteins.

Kresten Lindorff-Larsen, Jesper Ferkinghoff-Borg, K. Lindorff-Larsen, 2008, Biophysical journal.

Recognizing and defining true Ras binding domains II: in silico prediction based on homology modelling and energy calculations.

Joost Schymkowitz, Frederic Rousseau, Jesper Ferkinghoff-Borg, 2005, Journal of molecular biology.

Resource Kinome-wide Decoding of Network-Attacking Mutations Rewiring Cancer Signaling Graphical Abstract Highlights

Chad J. Miller, M. Helmer-Citterich, R. Linding, 2015 .

Probability-based detection of phosphoproteomic uncertainty reveals rare signaling events driven by oncogenic kinase gene fusion

E. Klipp, R. Linding, J. Ferkinghoff-Borg, 2019, bioRxiv.

An efficient null model for conformational fluctuations in proteins.

Sandro Bottaro, T. Hamelryck, J. Ferkinghoff-Borg, 2012, Structure.

Lipid Modulation of a Class B GPCR: Elucidating the Modulatory Role of PI(4, 5)P2 Lipids

Nils A. Berglund, C. Robinson, J. Ferkinghoff-Borg, 2022, J. Chem. Inf. Model..

Dynamics of crystal formation in the Greenland NorthGRIP ice core

M. Jensen, M. Levinsen, J. Mathiesen, 2003, Journal of Glaciology.

Diffusion, fragmentation, and coagulation processes: analytical and numerical results.

M. Jensen, J. Mathiesen, J. Ferkinghoff-Borg, 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

Scale-free cluster distributions from conserving merging-fragmentation processes

M. Jensen, J. Mathiesen, J. Ferkinghoff-Borg, 2005, cond-mat/0508067.

B M ] 1 2 D ec 2 00 5 What thermodynamic features characterize good and bad folders ? Results from a simplified off – lattice protein model

R. Broglia, G. Tiana, J. Ferkinghoff-Borg, 2013 .

Thermodynamic features characterizing good and bad folding sequences obtained using a simplified off-lattice protein model.

R. Broglia, G. Tiana, J. Ferkinghoff-Borg, 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

Probabilistic Determination of Native State Ensembles of Proteins.

Kresten Lindorff-Larsen, Wouter Boomsma, Jesper Ferkinghoff-Borg, 2014, Journal of chemical theory and computation.

Neural mechanism of activity spread in the cat motor cortex and its relation to the intrinsic connectivity

Jesper Ferkinghoff-Borg, Christian Ethier, Charles Capaday, 2011, The Journal of physiology.

The FoldX web server: an online force field

François Stricher, Luis Serrano, Joost Schymkowitz, 2005, Nucleic Acids Res..

Compact phases of polymers with hydrogen bonding.

M. Jensen, J. Ferkinghoff-Borg, A. Trovato, 2001, Physical review. E, Statistical, nonlinear, and soft matter physics.

SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs

François Stricher, Luis Serrano, Jesper Ferkinghoff-Borg, 2004, Nucleic Acids Res..

Deep neural networks identify signaling mechanisms of ErbB-family drug resistance from a continuous cell morphology space.

R. Linding, J. Ferkinghoff-Borg, I. Horak, 2021, Cell reports.

Dynamic Rearrangement of Cell States Detected by Systematic Screening of Sequential Anticancer Treatments.

Jesper Ferkinghoff-Borg, Thomas R Cox, Rune Linding, 2017, Cell reports.

Novel optical and statistical methods reveal colloid-wall interactions inconsistent with DLVO and Lifshitz theories.

Jakob K. Dreyer, L. Oddershede, J. Ferkinghoff-Borg, 2005, Journal of colloid and interface science.

Microbial Biofilm as a Smart Material

Jesper Ferkinghoff-Borg, Christian Garde, Martin Welch, 2015, Sensors.

Size of quorum sensing communities.

J. Ferkinghoff-Borg, T. Sams, 2014, Molecular bioSystems.

Kinetic Model for Signal Binding to the Quorum Sensing Regulator LasR

M. Welch, J. Ferkinghoff-Borg, M. Givskov, 2013, International journal of molecular sciences.

Quorum sensing regulation in Aeromonas hydrophila.

Kim Sneppen, Jesper Ferkinghoff-Borg, Thomas Bjarnsholt, 2010, Journal of molecular biology.

Computational Redesign of Thioredoxin Is Hypersensitive toward Minor Conformational Changes in the Backbone Template.

Kresten Lindorff-Larsen, Jesper Ferkinghoff-Borg, Thomas Hamelryck, 2016, Journal of molecular biology.

Genome-Wide Prediction of SH2 Domain Targets Using Structural Information and the FoldX Algorithm

Ignacio E. Sánchez, François Stricher, Pedro Beltrão, 2008, PLoS Comput. Biol..

Subtle Monte Carlo Updates in Dense Molecular Systems.

Wouter Boomsma, Sandro Bottaro, Jesper Ferkinghoff-Borg, 2012, Journal of chemical theory and computation.

Diffusion, fragmentation and merging: Rate equations, distributions and critical points

M. Jensen, J. Mathiesen, J. Ferkinghoff-Borg, 2006 .

Combining Experiments and Simulations Using the Maximum Entropy Principle

Kresten Lindorff-Larsen, Wouter Boomsma, Jesper Ferkinghoff-Borg, 2014, PLoS Comput. Biol..

PHAISTOS: A framework for Markov chain Monte Carlo simulation and inference of protein structure

Kresten Lindorff-Larsen, Pengfei Tian, Jan H. Jensen, 2013, J. Comput. Chem..

Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models

Jesper Ferkinghoff-Borg, Thomas Hamelryck, Christian Andreetta, 2010, BMC Bioinformatics.

Generative probabilistic models extend the scope of inferential structure determination.

Simon Olsson, Wouter Boomsma, Jes Frellsen, 2011, Journal of magnetic resonance.

A Probabilistic Model of RNA Conformational Space

Kanti V. Mardia, Jes Frellsen, Jesper Ferkinghoff-Borg, 2009, PLoS Comput. Biol..

General Protocol for Constructing Molecular Models of Nanodiscs

Tsjerk A. Wassenaar, Jesper Ferkinghoff-Borg, Leonardo De Maria, 2021, J. Chem. Inf. Model..

Denatured state is critical in determining the properties of model proteins designed on different folds

G. Tiana, J. Ferkinghoff-Borg, R. Broglia, 2008, Proteins.

Robust Estimation of Diffusion-Optimized Ensembles for Enhanced Sampling.

Kresten Lindorff-Larsen, Jesper Ferkinghoff-Borg, Anders Irbäck, 2014, Journal of chemical theory and computation.

A probabilistic model of RNA conformational space A Probabilistic Model of RNA Conformational Space

K. Mardia, J. Frellsen, I. Moltke, 2009 .

SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks.

M Ander, P Beltrao, B Di Ventura, 2004, Systems biology.

Bowhead: Bayesian modelling of cell velocity during concerted cell migration

Xavier Robin, Jesper Ferkinghoff-Borg, Rune Linding, 2018, PLoS Comput. Biol..

Stop-and-go kinetics in amyloid fibrillation.

S. Krishna, M. Jensen, D. Otzen, 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.

Bayesian Methods in Structural Bioinformatics

Kanti V. Mardia, Jesper Ferkinghoff-Borg, Thomas Hamelryck, 2012 .

Bayesian Generalised Ensemble Markov Chain Monte Carlo

Ole Winther, Zoubin Ghahramani, Jes Frellsen, 2016, AISTATS.

Computational Redesign of Thioredoxin Is Hypersensitive toward Minor Conformational Changes in the Backbone Template.

K. E. Johansson, K. Lindorff-Larsen, T. Hamelryck, 2016, Journal of molecular biology.

Optimized Monte Carlo analysis for generalized ensembles

J. Ferkinghoff-Borg, J. Ferkinghoff-Borg, 2002 .

Probabilistic thermal stability prediction through sparsity promoting transformer representation

J. Ferkinghoff-Borg, Per Greisen, Nikolai Lorenzen, 2022, ArXiv.

Information theoretical quantification of cooperativity in signalling complexes

Tom Lenaerts, Jesper Ferkinghoff-Borg, Joost Schymkowitz, 2009, BMC Systems Biology.

K. Lindorff-Larsen, J. Ferkinghoff-Borg, 2009, PloS one.

Diffusion, fragmentation and merging processes in ice crystals, alpha helices and other systems

M. Jensen, J. Mathiesen, J. Ferkinghoff-Borg, 2006 .

Competition between diffusion and fragmentation: an important evolutionary process of nature.

M. Jensen, K. Sneppen, J. Mathiesen, 2003, Physical review letters.