Jesper Ferkinghoff-Borg

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Thomas HamelryckBioinformatics center, University of CopenhagenVerified email at binf.ku.dk
Luis SerranoProfesor de cine, Imagen y Sonido Verified email at eiso.es
Wouter BoomsmaAssociate Professor, Department of Computer Science, University of CopenhagenVerified email at di.ku.dk
Jes FrellsenAssociate Professor, Technical University of Denmark (DTU)Verified email at dtu.dk
Kresten Lindorff-LarsenLinderstrøm-Lang Centre for Protein Science, Department of Biology, University of CopenhagenVerified email at bio.ku.dk
Kanti MardiaSENIOR RESARCH PROFESSOR ,UNIVERSITY OF LEEDS AND UNIVERSITY OF OXFORDVerified email at leeds.ac.uk
Mogens H. JensenProfessor of Complex Systems, Niels Bohr InstituteVerified email at nbi.dk
Dr. Rune LindingHumboldt-Universität zu BerlinVerified email at hu-berlin.de
Christian AndreettaUniv. of Copenhagen, Denmark, and Uni Computing, Uni Research, NorwayVerified email at uni.no
Sandro BottaroUniversity of CopenhagenVerified email at bio.ku.dk
Poul OlesenEmeritus Professor of Theoretical Physics, Niels Bohr InstituteVerified email at nbi.dk
Thomas SamsTechnical University of DenmarkVerified email at dtu.dk
Kim SneppenProfessor at Niels Bohr Institute, Copenhagen UniversityVerified email at nbi.dk
Simon OlssonAssistant Professor, Chalmers University of TechnologyVerified email at chalmers.se
Guido TianaUniversity of MilanoVerified email at unimi.it
Pengfei TianProtein Design Scientist at Novozymes A/SVerified email at nih.gov
Pedro BeltraoGroup Leader, EMBL-EBIVerified email at ebi.ac.uk
Tim HarderResearch Scientist at Philips ResearchVerified email at philips.com
Kristoffer Enøe JohanssonDepartment of Pharmacy, University of CopenhagenVerified email at sund.ku.dk
Thomas R. CoxGarvan Institute of Medical ResearchVerified email at garvan.org.au

Jesper Ferkinghoff-Borg

Associate Professor, Principal Scientist, Novo Nordisk A/S

Verified email at novonordisk.com

Machine Learning Deep Learning protein dynamics - protein interaction networks - cellular communication - automatisation


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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	1611	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	344	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	166	2008
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	165	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	162	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	142	2015
Combining experiments and simulations using the maximum entropy principle W Boomsma, J Ferkinghoff-Borg, K Lindorff-Larsen PLoS Comput Biol 10 (2), e1003406, 2014	128	2014
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	120	2005
A probabilistic model of RNA conformational space J Frellsen, I Moltke, M Thiim, KV Mardia, J Ferkinghoff-Borg, T Hamelryck PLoS Comput Biol 5 (6), e1000406, 2009	102	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	81	2010
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), 1-14, 2010	60	2010
Similarity measures for protein ensembles K Lindorff-Larsen, J Ferkinghoff-Borg PloS one 4 (1), e4203, 2009	50	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	49	2008
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	48	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 Comput Biol 4 (4), e1000052, 2008	47	2008
Optimized Monte Carlo analysis for generalized ensembles J Ferkinghoff-Borg The European Physical Journal B-Condensed Matter and Complex Systems 29 (3 …, 2002	47	2002
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	44	2010
Probabilistic determination of native state ensembles of proteins S Olsson, BR Vögeli, A Cavalli, W Boomsma, J Ferkinghoff-Borg, ... Journal of Chemical Theory and Computation 10 (8), 3484-3491, 2014	40	2014
Bayesian methods in structural bioinformatics T Hamelryck, K Mardia, J Ferkinghoff-Borg Springer, 2012	40	2012
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	36	2013

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