Jesper Ferkinghoff-Borg
Jesper Ferkinghoff-Borg
Associate Professor, Research Director, Novo Nordisk A/S
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The FoldX web server: an online force field
J Schymkowitz, J Borg, F Stricher, R Nys, F Rousseau, L Serrano
Nucleic acids research 33 (suppl_2), W382-W388, 2005
Prediction of water and metal binding sites and their affinities by using the Fold-X force field
JWH Schymkowitz, F Rousseau, IC Martins, J Ferkinghoff-Borg, F Stricher, ...
Proceedings of the National Academy of Sciences 102 (29), 10147-10152, 2005
A generative, probabilistic model of local protein structure
W Boomsma, KV Mardia, CC Taylor, J Ferkinghoff-Borg, A Krogh, ...
Proceedings of the National Academy of Sciences 105 (26), 8932-8937, 2008
Combining experiments and simulations using the maximum entropy principle
W Boomsma, J Ferkinghoff-Borg, K Lindorff-Larsen
PLoS computational biology 10 (2), e1003406, 2014
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, J Ferkinghoff-Borg, M Foglierini, ...
Systems biology 1 (1), 129-138, 2004
SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs
J Reumers, J Schymkowitz, J Ferkinghoff-Borg, F Stricher, L Serrano, ...
Nucleic acids research 33 (suppl_1), D527-D532, 2005
Kinome-wide decoding of network-attacking mutations rewiring cancer signaling
P Creixell, EM Schoof, CD Simpson, J Longden, CJ Miller, HJ Lou, ...
Cell 163 (1), 202-217, 2015
Recognizing and defining true Ras binding domains II: in silico prediction based on homology modelling and energy calculations
C Kiel, S Wohlgemuth, F Rousseau, J Schymkowitz, J Ferkinghoff-Borg, ...
Journal of molecular biology 348 (3), 759-775, 2005
A probabilistic model of RNA conformational space
J Frellsen, I Moltke, M Thiim, KV Mardia, J Ferkinghoff-Borg, T Hamelryck
PLoS computational biology 5 (6), e1000406, 2009
Potentials of mean force for protein structure prediction vindicated, formalized and generalized
T Hamelryck, M Borg, M Paluszewski, J Paulsen, J Frellsen, C Andreetta, ...
PloS one 5 (11), e13714, 2010
Similarity measures for protein ensembles
K Lindorff-Larsen, J Ferkinghoff-Borg
PloS one 4 (1), e4203, 2009
Experimental parameterization of an energy function for the simulation of unfolded proteins
AB Norgaard, J Ferkinghoff-Borg, K Lindorff-Larsen
Biophysical journal 94 (1), 182-192, 2008
Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models
K Stovgaard, C Andreetta, J Ferkinghoff-Borg, T Hamelryck
BMC bioinformatics 11, 1-14, 2010
Bayesian methods in structural bioinformatics
T Hamelryck, K Mardia, J Ferkinghoff-Borg
Springer, 2012
Quorum sensing regulation in Aeromonas hydrophila
C Garde, T Bjarnsholt, M Givskov, TH Jakobsen, M Hentzer, A Claussen, ...
Journal of molecular biology 396 (4), 849-857, 2010
Stop-and-go kinetics in amyloid fibrillation
J Ferkinghoff-Borg, J Fonslet, CB Andersen, S Krishna, S Pigolotti, H Yagi, ...
Physical Review E 82 (1), 010901, 2010
Genome-wide prediction of SH2 domain targets using structural information and the FoldX algorithm
IE Sánchez, P Beltrao, F Stricher, J Schymkowitz, J Ferkinghoff-Borg, ...
PLoS computational biology 4 (4), e1000052, 2008
Optimized Monte Carlo analysis for generalized ensembles
J Ferkinghoff-Borg
The European Physical Journal B-Condensed Matter and Complex Systems 29, 481-484, 2002
PHAISTOS: a framework for Markov chain Monte Carlo simulation and inference of protein structure
W Boomsma, J Frellsen, T Harder, S Bottaro, KE Johansson, P Tian, ...
Journal of computational chemistry 34 (19), 1697-1705, 2013
Quantifying information transfer by protein domains: analysis of the Fyn SH2 domain structure
T Lenaerts, J Ferkinghoff-Borg, F Stricher, L Serrano, JWH Schymkowitz, ...
BMC structural biology 8, 1-15, 2008
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