Arne Elofsson

65 papers A* 2C 1Journal 61Unranked 1
YearRankTypeTitle / Venue / Authors
2026 J jnl
A deep learning framework for comprehensive prediction of human RNA G-quadruplex-binding proteins.
Bioinform.
Serena Rosignoli, Sophie Taraglio, Francesco Di Luzio, Elisa Lustrino, Dario F. Marzella, Arne Elofsson, Massimo Panella, Alessandro Paiardini
2026 J jnl
Evaluating deep learning based structure prediction methods on antibody-antigen complexes.
Bioinform.
Samuel Fromm, Marko Ludaic, Arne Elofsson
2025 A* conf
Energy-Based Flow Matching for Generating 3D Molecular Structure.
ICML
Wenyin Zhou, Christopher Iliffe Sprague, Vsevolod Viliuga, Matteo Tadiello, Arne Elofsson, Hossein Azizpour
2025 J jnl
Energy-Based Flow Matching for Generating 3D Molecular Structure.
CoRR
Wenyin Zhou, Christopher Iliffe Sprague, Vsevolod Viliuga, Matteo Tadiello, Arne Elofsson, Hossein Azizpour
2025 J jnl
Flexibility-Conditioned Protein Structure Design with Flow Matching.
CoRR
Vsevolod Viliuga, Leif Seute, Nicolas Wolf, Simon Wagner, Arne Elofsson, Jan Stühmer, Frauke Gräter
2025 A* conf
Flexibility-conditioned protein structure design with flow matching.
ICML
Vsevolod Viliuga, Leif Seute, Nicolas Wolf, Simon Wagner, Arne Elofsson, Jan Stühmer, Frauke Gräter
2024 J jnl
Hessian-Informed Flow Matching.
CoRR
Christopher Iliffe Sprague, Arne Elofsson, Hossein Azizpour
2024 J jnl
M-Ionic: prediction of metal-ion-binding sites from sequence using residue embeddings.
Bioinform.
Aditi Shenoy, Yogesh Kalakoti, Durai Sundar, Arne Elofsson
2024 J jnl
MoLPC2: improved prediction of large protein complex structures and stoichiometry using Monte Carlo Tree Search and AlphaFold2.
Bioinform.
Ho Yeung Chim, Arne Elofsson
2024 J jnl
Opportunities for machine learning in scientific discovery.
CoRR
Ricardo Vinuesa, Jean Rabault, Hossein Azizpour, Stefan Bauer, Bingni W. Brunton, Arne Elofsson, Elias Jarlebring, Hedvig Kjellström, Stefano Markidis, David Marlevi, Paola Cinnella, Steven L. Brunton
2024 J jnl
Stable Autonomous Flow Matching.
CoRR
Christopher Iliffe Sprague, Arne Elofsson, Hossein Azizpour
2023 J jnl
AFTGAN: prediction of multi-type PPI based on attention free transformer and graph attention network.
Bioinform.
Yanlei Kang, Arne Elofsson, Yunliang Jiang, Weihong Huang, Minzhe Yu, Zhong Li
2023 J jnl
Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes.
Bioinform.
Wensi Zhu, Aditi Shenoy, Petras Kundrotas, Arne Elofsson
2022 J jnl
DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation.
Nucleic Acids Res.
Federica Quaglia, Bálint Mészáros, Edoardo Salladini, András Hatos, Rita Pancsa, Lucía B. Chemes, Mátyás Pajkos, Tamas Lazar, Samuel Peña-Díaz, Jaime Santos, Veronika Ács, Nazanin Farahi, Erzsébet Fichó, Maria Cristina Aspromonte, Claudio Bassot, Anastasia Chasapi, Norman E. Davey, Radoslav Davidovic, Laszlo Dobson, Arne Elofsson, Gábor Erdös, Pascale Gaudet, Michelle G. Giglio, Juliana Glavina, Javier Iserte, Valentín Iglesias, Zsófia L. Kálmán, Matteo Lambrughi, Emanuela Leonardi, Sonia Longhi, Sandra Macedo-Ribeiro, Emiliano Maiani, Julia Marchetti, Cristina Marino Buslje, Attila Meszaros, Alexander Miguel Monzon, Giovanni Minervini, Suvarna Nadendla, Juliet F. Nilsson, Marián Novotný, Christos A. Ouzounis, Nicolas Palopoli, Elena Papaleo, Pedro J. Barbosa Pereira, Gabriele Pozzati, Vasilis J. Promponas, Jordi Pujols, Alma Carolina Sanchez Rocha, Martin Salas, Luciana Rodriguez Sawicki, Éva Schád, Aditi Shenoy, Tamás Szaniszló, Konstantinos D. Tsirigos, Nevena Veljkovic, Gustavo D. Parisi, Salvador Ventura, Zsuzsanna Dosztányi, Peter Tompa, Silvio C. E. Tosatto, Damiano Piovesan
2022 J jnl
Limits and potential of combined folding and docking.
Bioinform.
Gabriele Pozzati, Wensi Zhu, Claudio Bassot, John Lamb, Petras Kundrotas, Arne Elofsson
2021 J jnl
Accurate contact-based modelling of repeat proteins predicts the structure of new repeats protein families.
PLoS Comput. Biol.
Claudio Bassot, Arne Elofsson
2021 J jnl
GCSENet: A GCN, CNN and SENet ensemble model for microRNA-disease association prediction.
PLoS Comput. Biol.
Zhong Li, Kaiyancheng Jiang, Shengwei Qin, Yijun Zhong, Arne Elofsson
2021 J jnl
GraphQA: protein model quality assessment using graph convolutional networks.
Bioinform.
Federico Baldassarre, David Menéndez Hurtado, Arne Elofsson, Hossein Azizpour
2021 J jnl
Protein sequence-to-structure learning: Is this the end(-to-end revolution)?
CoRR
Elodie Laine, Stephan Eismann, Arne Elofsson, Sergei Grudinin
2021 J jnl
The evolutionary history of topological variations in the CPA/AT transporters.
PLoS Comput. Biol.
Govindarajan Sudha, Claudio Bassot, John Lamb, Nanjiang Shu, Yan Huang, Arne Elofsson
2021 J jnl
Toward Characterising the Cellular 3D-Proteome.
Frontiers Bioinform.
Arne Elofsson
2021 J jnl
pyconsFold: a fast and easy tool for modeling and docking using distance predictions.
Bioinform.
John Lamb, Arne Elofsson
2020 J jnl
DisProt: intrinsic protein disorder annotation in 2020.
Nucleic Acids Res.
András Hatos, Borbála Hajdu-Soltész, Alexander Miguel Monzon, Nicolas Palopoli, Lucía Álvarez, Burcu Aykaç Fas, Claudio Bassot, Guillermo I. Benítez, Martina Bevilacqua, Anastasia Chasapi, Lucía B. Chemes, Norman E. Davey, Radoslav Davidovic, A. Keith Dunker, Arne Elofsson, Julien Gobeill, Nicolás S. González Foutel, Govindarajan Sudha, Mainak Guharoy, Tamás Horváth, Valentin Iglesias, Andrey V. Kajava, Orsolya P. Kovács, John Lamb, Matteo Lambrughi, Tamas Lazar, Jeremy Y. Leclercq, Emanuela Leonardi, Sandra Macedo-Ribeiro, Mauricio Macossay-Castillo, Emiliano Maiani, José A. Manso, Cristina Marino Buslje, Elizabeth Martínez-Pérez, Bálint Mészáros, Ivan Micetic, Giovanni Minervini, Nikoletta Murvai, Marco Necci, Christos A. Ouzounis, Mátyás Pajkos, Lisanna Paladin, Rita Pancsa, Elena Papaleo, Gustavo D. Parisi, Emilie Pasche, Pedro J. Barbosa Pereira, Vasilis J. Promponas, Jordi Pujols, Federica Quaglia, Patrick Ruch, Marco Salvatore, Éva Schád, Beáta Szabó, Tamás Szaniszló, Stella Tamana, Ágnes Tantos, Nevena Veljkovic, Salvador Ventura, Wim F. Vranken, Zsuzsanna Dosztányi, Peter Tompa, Silvio C. E. Tosatto, Damiano Piovesan
2020 J jnl
TransformerCPI: improving compound-protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments.
Bioinform.
Lifan Chen, Xiaoqin Tan, Dingyan Wang, Feisheng Zhong, Xiaohong Liu, Tianbiao Yang, Xiaomin Luo, Kaixian Chen, Hualiang Jiang, Mingyue Zheng, Arne Elofsson
2019 J jnl
PconsC4: fast, accurate and hassle-free contact predictions.
Bioinform.
Mirco Michel, David Menéndez Hurtado, Arne Elofsson
2019 J jnl
Ten simple rules on how to create open access and reproducible molecular simulations of biological systems.
PLoS Comput. Biol.
Arne Elofsson, Berk Hess, Erik Lindahl, Alexey Onufriev, David van der Spoel, Anders Wallqvist
2019 J jnl
Why do eukaryotic proteins contain more intrinsically disordered regions?
PLoS Comput. Biol.
Walter Basile, Marco Salvatore, Claudio Bassot, Arne Elofsson
2017 J jnl
DisProt 7.0: a major update of the database of disordered proteins.
Nucleic Acids Res.
Damiano Piovesan, Francesco Tabaro, Ivan Micetic, Marco Necci, Federica Quaglia, Christopher J. Oldfield, Maria Cristina Aspromonte, Norman E. Davey, Radoslav Davidovic, Zsuzsanna Dosztányi, Arne Elofsson, Alessandra Gasparini, András Hatos, Andrey V. Kajava, Lajos Kalmár, Emanuela Leonardi, Tamas Lazar, Sandra Macedo-Ribeiro, Mauricio Macossay-Castillo, Attila Meszaros, Giovanni Minervini, Nikoletta Murvai, Jordi Pujols, Daniel B. Roche, Edoardo Salladini, Éva Schád, Antoine Schramm, Beáta Szabó, Ágnes Tantos, Fiorella Tonello, Konstantinos D. Tsirigos, Nevena Veljkovic, Salvador Ventura, Wim F. Vranken, Per Warholm, Vladimir N. Uversky, A. Keith Dunker, Sonia Longhi, Peter Tompa, Silvio C. E. Tosatto
2017 J jnl
GWAR: robust analysis and meta-analysis of genome-wide association studies.
Bioinform.
Niki L. Dimou, Konstantinos D. Tsirigos, Arne Elofsson, Pantelis G. Bagos
2017 J jnl
High GC content causes orphan proteins to be intrinsically disordered.
PLoS Comput. Biol.
Walter Basile, Oxana Sachenkova, Sara Light, Arne Elofsson
2017 J jnl
Large-scale structure prediction by improved contact predictions and model quality assessment.
Bioinform.
Mirco Michel, David Menéndez Hurtado, Karolis Uziela, Arne Elofsson
2017 J jnl
Predicting accurate contacts in thousands of Pfam domain families using PconsC3.
Bioinform.
Mirco Michel, Marcin J. Skwark, David Menéndez Hurtado, Magnus Ekeberg, Arne Elofsson
2017 J jnl
ProQ3D: improved model quality assessments using deep learning.
Bioinform.
Karolis Uziela, David Menéndez Hurtado, Nanjiang Shu, Björn Wallner, Arne Elofsson
2017 J jnl
SubCons: a new ensemble method for improved human subcellular localization predictions.
Bioinform.
Marco Salvatore, Per Warholm, Nanjiang Shu, Walter Basile, Arne Elofsson
2016 J jnl
Improved topology prediction using the terminal hydrophobic helices rule.
Bioinform.
Christoph Peters, Konstantinos D. Tsirigos, Nanjiang Shu, Arne Elofsson
2016 J jnl
Inclusion of dyad-repeat pattern improves topology prediction of transmembrane β-barrel proteins.
Bioinform.
Sikander Hayat, Christoph Peters, Nanjiang Shu, Konstantinos D. Tsirigos, Arne Elofsson
2016 J jnl
PRED-TMBB2: improved topology prediction and detection of beta-barrel outer membrane proteins.
Bioinform.
Konstantinos D. Tsirigos, Arne Elofsson, Pantelis G. Bagos
2015 J jnl
The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides.
Nucleic Acids Res.
Konstantinos D. Tsirigos, Christoph Peters, Nanjiang Shu, Lukas Käll, Arne Elofsson
2014 J jnl
Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns.
PLoS Comput. Biol.
Marcin J. Skwark, Daniele Raimondi, Mirco Michel, Arne Elofsson
2014 J jnl
PconsFold: improved contact predictions improve protein models.
Bioinform.
Mirco Michel, Sikander Hayat, Marcin J. Skwark, Chris Sander, Debora S. Marks, Arne Elofsson
2013 J jnl
PconsC: combination of direct information methods and alignments improves contact prediction.
Bioinform.
Marcin J. Skwark, Abbi Abdel-Rehim, Arne Elofsson
2013 J jnl
PconsD: ultra rapid, accurate model quality assessment for protein structure prediction.
Bioinform.
Marcin J. Skwark, Arne Elofsson
2012 J jnl
BOCTOPUS: improved topology prediction of transmembrane β barrel proteins.
Bioinform.
Sikander Hayat, Arne Elofsson
2012 J jnl
Ranking models of transmembrane
Bioinform.
Sikander Hayat, Arne Elofsson
2011 J jnl
Improved predictions by Pcons.net using multiple templates.
Bioinform.
Per Larsson, Marcin J. Skwark, Björn Wallner, Arne Elofsson
2011 J jnl
KalignP: Improved multiple sequence alignments using position specific gap penalties in Kalign2.
Bioinform.
Nanjiang Shu, Arne Elofsson
2011 J jnl
Rapid membrane protein topology prediction.
Bioinform.
Aron Hennerdal, Arne Elofsson
2010 J jnl
MPRAP: An accessibility predictor for alpha-helical transmembrane proteins that performs well inside and outside the membrane.
BMC Bioinform.
Kristoffer Illergård, Simone Callegari, Arne Elofsson
2009 J jnl
TOPCONS: consensus prediction of membrane protein topology.
Nucleic Acids Res.
Andreas Bernsel, Håkan Viklund, Aron Hennerdal, Arne Elofsson
2008 J jnl
OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar.
Bioinform.
Håkan Viklund, Arne Elofsson
2008 J jnl
SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology.
Bioinform.
Håkan Viklund, Andreas Bernsel, Marcin J. Skwark, Arne Elofsson
2007 J jnl
Pcons.net: protein structure prediction meta server.
Nucleic Acids Res.
Björn Wallner, Per Larsson, Arne Elofsson
2006 J jnl
Expansion of Protein Domain Repeats.
PLoS Comput. Biol.
Åsa K. Björklund, Diana Ekman, Arne Elofsson
2006 J jnl
Improved alignment quality by combining evolutionary information, predicted secondary structure and self-organizing maps.
BMC Bioinform.
Tomas Ohlson, Varun Aggarwal, Arne Elofsson, Robert M. MacCallum
2006 J jnl
PONGO: a web server for multiple predictions of all-alpha transmembrane proteins.
Nucleic Acids Res.
Mauro Amico, Michele Finelli, Ivan Rossi, Andrea Zauli, Arne Elofsson, Håkan Viklund, Gunnar von Heijne, David Jones, Anders Krogh, Piero Fariselli, Pier Luigi Martelli, Rita Casadio
2006 — conf
ZPRED: Predicting the distance to the membrane center for residues in alpha-helical membrane proteins.
ISMB (Supplement of Bioinformatics)
Erik Granseth, Håkan Viklund, Arne Elofsson
2005 J jnl
Pcons5: combining consensus, structural evaluation and fold recognition scores.
Bioinform.
Björn Wallner, Arne Elofsson
2005 J jnl
ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins.
BMC Bioinform.
Tomas Ohlson, Arne Elofsson
2003 J jnl
3D-Jury: A Simple Approach to Improve Protein Structure Predictions.
Bioinform.
Krzysztof Ginalski, Arne Elofsson, Daniel Fischer, Leszek Rychlewski
2002 J jnl
Prediction of MHC class I binding peptides, using SVMHC.
BMC Bioinform.
Pierre Dönnes, Arne Elofsson
2001 J jnl
A study of quality measures for protein threading models.
BMC Bioinform.
Susana Cristobal, Adam T. Zemla, Daniel Fischer, Leszek Rychlewski, Arne Elofsson
2001 C conf
Side Chain-Positioning as an Integer Programming Problem.
WABI
Olivia Eriksson, Yishao Zhou, Arne Elofsson
2001 J jnl
Structure prediction meta server.
Bioinform.
Janusz M. Bujnicki, Arne Elofsson, Daniel Fischer, Leszek Rychlewski
2000 J jnl
MaxSub: an automated measure for the assessment of protein structure prediction quality.
Bioinform.
Naomi Siew, Arne Elofsson, Leszek Rychlewski, Daniel Fischer
1999 J jnl
A comparison of sequence and structure protein domain families as a basis for structural genomics.
Bioinform.
Arne Elofsson, Erik L. L. Sonnhammer