Erik Lindahl - RankMe

46 papers A 3Journal 33Unranked 10

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Cryo-EM ligand building using AlphaFold3-like model and molecular dynamics. PLoS Comput. Biol. Nandan Haloi, Rebecca J. Howard, Erik Lindahl
2025	J	`jnl`	Estimation of Absolute Binding Free Energies for Drugs That Bind Multiple Proteins. J. Chem. Inf. Model. Erik Lindahl, Ran Friedman
2025	J	`jnl`	Lossy Compression of Scientific Data: Applications Constrains and Requirements. CoRR Franck Cappello, Allison H. Baker, Ebru Bozdag, Martin Burtscher, Kyle Chard, Sheng Di, Paul Christopher O'Grady, Peng Jiang, Shaomeng Li, Erik Lindahl, Peter Lindstrom, Magnus Lundborg, Kai Zhao, Xin Liang, Masaru Nagaso, Kento Sato, Amarjit Singh, Seung Woo Son, Dingwen Tao, Jiannan Tian, Robert Underwood, Kazutomo Yoshii, Danylo Lykov, Yuri Alexeev, Kyle Gerard Felker
2025	J	`jnl`	Resolving the conformational ensemble of a membrane protein by integrating small-angle scattering with AlphaFold. PLoS Comput. Biol. Samuel Eriksson Lidbrink, Rebecca J. Howard, Nandan Haloi, Erik Lindahl
2025	A	`conf`	What to Support When You're Compressing: The State of Practice Gaps and Opportunities for Scientific Data Compression. SC Franck Cappello, Robert Underwood, Yuri Alexeev, Allison H. Baker, Ebru Bozdag, Martin Burtscher, Kyle Chard, Sheng Di, Kyle Gerard Felker, Paul Christopher O'Grady, Hanqi Guo, Yafan Huang, Peng Jiang, Sian Jin, Petter Johansson, Shaomeng Li, Xin Liang, Erik Lindahl, Peter Lindstrom, Zarija Lukic, Magnus Lundborg, Danylo Lykov, Masaru Nagaso, Kento Sato, Amarjit Singh, Seung Woo Son, Shihui Song, William Tang, Dingwen Tao, Jiannan Tian, Kazutomo Yoshii, Kai Zhao
2024	—	`conf`	GROMACS on AMD GPU-Based HPC Platforms: Using SYCL for Performance and Portability. CUG Andrey Alekseenko, Szilárd Páll, Erik Lindahl
2024	J	`jnl`	GROMACS on AMD GPU-Based HPC Platforms: Using SYCL for Performance and Portability. CoRR Andrey Alekseenko, Szilárd Páll, Erik Lindahl
2024	—	`conf`	LIGATE - LIgand Generator and portable drug discovery platform AT Exascale. CF (Companion) Gianluca Palermo, Gianmarco Accordi, Davide Gadioli, Yuedong Zhang, Emanuele Vitali, Bruno Guindani, Danilo Ardagna, Cristina Silvano, Andrea Rosario Beccari, Domenico Bonanni, Carmine Talarico, Filippo Lunghini, Akash Deep Biswas, Jan Martinovic, Martin Golasowski, Paulo Silva, Ada Böhm, Jakub Beránek, Jan Krenek, Branislav Jansik, Peter Thoman, Philip Salzmann, Thomas Fahringer, Torsten Schwede, Leila Tamara Alexander, Gerardo Tauriello, Janani Durairaj, Biagio Cosenza, Luigi Crisci, Andrew Emerson, Federico Ficarelli, Erik Lindahl, Sebastian Wingbermühle, Daniele Gregori, Silvano Coletti, Emanuele Sana, Philipp Gschwandtner
2024	J	`jnl`	Simulating the Skin Permeation Process of Ionizable Molecules. J. Chem. Inf. Model. Magnus Lundborg, Christian Wennberg, Erik Lindahl, Lars Norlén
2023	J	`jnl`	Gentle and fast all-atom model refinement to cryo-EM densities via a maximum likelihood approach. PLoS Comput. Biol. Christian Blau, Linnea Yvonnesdotter, Erik Lindahl
2023	—	`conf`	Tunable and Portable Extreme-Scale Drug Discovery Platform at Exascale: the LIGATE Approach. CF Gianluca Palermo, Gianmarco Accordi, Davide Gadioli, Emanuele Vitali, Cristina Silvano, Bruno Guindani, Danilo Ardagna, Andrea Rosario Beccari, Domenico Bonanni, Carmine Talarico, Filippo Lunghini, Jan Martinovic, Paulo Silva, Ada Bohm, Jakub Beránek, Jan Krenek, Branislav Jansik, Biagio Cosenza, Luigi Crisci, Peter Thoman, Philip Salzmann, Thomas Fahringer, Leila T. Alexander, Gerardo Tauriello, Torsten Schwede, Janani Durairaj, Andrew Emerson, Federico Ficarelli, Sebastian Wingbermühle, Erik Lindahl, Daniele Gregori, Emanuele Sana, Silvano Coletti, Philipp Gschwandtner
2023	J	`jnl`	Tunable and Portable Extreme-Scale Drug Discovery Platform at Exascale: the LIGATE Approach. CoRR Gianluca Palermo, Gianmarco Accordi, Davide Gadioli, Emanuele Vitali, Cristina Silvano, Bruno Guindani, Danilo Ardagna, Andrea Rosario Beccari, Domenico Bonanni, Carmine Talarico, Filippo Lunghini, Jan Martinovic, Paulo Silva, Ada Bohm, Jakub Beránek, Jan Krenek, Branislav Jansik, Luigi Crisci, Biagio Cosenza, Peter Thoman, Philip Salzmann, Thomas Fahringer, Leila T. Alexander, Gerardo Tauriello, Torsten Schwede, Janani Durairaj, Andrew Emerson, Federico Ficarelli, Sebastian Wingbermühle, Erik Lindahl, Daniele Gregori, Emanuele Sana, Silvano Coletti, Philipp Gschwandtner
2023	J	`jnl`	Understanding Drug Skin Permeation Enhancers Using Molecular Dynamics Simulations. J. Chem. Inf. Model. Christian Wennberg, Magnus Lundborg, Erik Lindahl, Lars Norlén
2021	—	`conf`	Experiences With Adding SYCL Support to GROMACS. IWOCL Andrey Alekseenko, Szilárd Páll, Erik Lindahl
2020	J	`jnl`	Heterogeneous Parallelization and Acceleration of Molecular Dynamics Simulations in GROMACS. CoRR Szilárd Páll, Artem A. Zhmurov, Paul Bauer, Mark James Abraham, Magnus Lundborg, Alan Gray, Berk Hess, Erik Lindahl
2019	J	`jnl`	Effective degrees of freedom for surface finish defect detection and classification. CoRR Natalya Pya Arnqvist, Blaise Ngendangenzwa, Erik Lindahl, Leif Nilsson, Jun Yu
2019	J	`jnl`	Sharing Data from Molecular Simulations. J. Chem. Inf. Model. Mark James Abraham, Rossen Apostolov, Jonathan Barnoud, Paul Bauer, Christian Blau, Alexandre M. J. J. Bonvin, Matthieu Chavent, John D. Chodera, Karmen Condic-Jurkic, Lucie Delemotte, Helmut Grubmüller, Rebecca J. Howard, E. Joseph Jordan, Erik Lindahl, Samuli Ollila, Jana Selent, Daniel G. A. Smith, Phillip J. Stansfeld, Johanna K. S. Tiemann, Mikaël Trellet, Christopher J. Woods, Artem A. Zhmurov
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	—	`conf`	The Future of Swedish e-Science: SeRC 2.0. eScience Erwin Laure, Olivia Eriksson, Erik Lindahl, Dan S. Henningson
2019	J	`jnl`	eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces. Bioinform. Laura Orellana, Johan Gustavsson, Cathrine Bergh, Ozge Yoluk, Erik Lindahl
2018	J	`jnl`	e-Science in Scandinavia - The Case of the Swedish e-Science Research Center. Inform. Spektrum Olivia Eriksson, Erwin Laure, Erik Lindahl, Dan S. Henningson, Anders Ynnerman
2017	J	`jnl`	Copernicus, a hybrid dataflow and peer-to-peer scientific computing platform for efficient large-scale ensemble sampling. Future Gener. Comput. Syst. Iman Pouya, Sander Pronk, Magnus Lundborg, Erik Lindahl
2016	J	`jnl`	The Molecular Basis of Polyunsaturated Fatty Acid Interactions with the PLoS Comput. Biol. Samira Yazdi, Matthias Stein, Fredrik Elinder, Magnus Andersson, Erik Lindahl
2015	J	`jnl`	Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS. CoRR Szilárd Páll, Mark James Abraham, Carsten Kutzner, Berk Hess, Erik Lindahl
2014	J	`jnl`	An efficient and extensible format, library, and API for binary trajectory data from molecular simulations. J. Comput. Chem. Magnus Lundborg, Rossen Apostolov, Daniel Spångberg, Anders Gärdenäs, David van der Spoel, Erik Lindahl
2014	—	`conf`	Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS. EASC Szilárd Páll, Mark James Abraham, Carsten Kutzner, Berk Hess, Erik Lindahl
2013	J	`jnl`	GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinform. Sander Pronk, Szilárd Páll, Roland Schulz, Per Larsson, Pär Bjelkmar, Rossen Apostolov, Michael R. Shirts, Jeremy C. Smith, Peter M. Kasson, David van der Spoel, Berk Hess, Erik Lindahl
2012	J	`jnl`	Improved model quality assessment using ProQ2. BMC Bioinform. Arjun Ray, Erik Lindahl, Björn Wallner
2012	J	`jnl`	Molecular Mechanism for the Dual Alcohol Modulation of Cys-loop Receptors. PLoS Comput. Biol. Samuel Murail, Rebecca J. Howard, Torben Broemstrup, Edward J. Bertaccini, R. Adron Harris, James R. Trudell, Erik Lindahl
2012	—	`conf`	Preparing Scientific Application Software for Exascale Computing. PARA J. A. Åström, Adam C. Carter, James Hetherington, K. Ioakimidis, Erik Lindahl, G. Mozdzynski, Rupert W. Nash, Philipp Schlatter, Artur Signell, Jan Westerholm
2011	A	`conf`	Copernicus: a new paradigm for parallel adaptive molecular dynamics. SC Sander Pronk, Per Larsson, Iman Pouya, Gregory R. Bowman, Imran S. Haque, Kyle Beauchamp, Berk Hess, Vijay S. Pande, Peter M. Kasson, Erik Lindahl
2011	—	`conf`	Poster: 3D tixels: a highly efficient algorithm for gpu/cpu-acceleration of molecular dynamics on heterogeneous parallel architectures. SC Companion Szilárd Páll, Berk Hess, Erik Lindahl
2010	J	`jnl`	A high-performance parallel-generalized born implementation enabled by tabulated interaction rescaling. J. Comput. Chem. Per Larsson, Erik Lindahl
2010	J	`jnl`	Atomic-Resolution Simulations Predict a Transition State for Vesicle Fusion Defined by Contact of a Few Lipid Tails. PLoS Comput. Biol. Peter M. Kasson, Erik Lindahl, Vijay S. Pande
2010	J	`jnl`	Model quality assessment for membrane proteins. Bioinform. Arjun Ray, Erik Lindahl, Björn Wallner
2010	J	`jnl`	Modeling Anesthetic Binding Sites within the Glycine Alpha One Receptor Based on Prokaryotic Ion Channel Templates: The Problem with TM4. J. Chem. Inf. Model. Edward J. Bertaccini, Björn Wallner, James R. Trudell, Erik Lindahl
2009	J	`jnl`	Conformational Changes and Slow Dynamics through Microsecond Polarized Atomistic Molecular Simulation of an Integral Kv1.2 Ion Channel. PLoS Comput. Biol. Pär Bjelkmar, Perttu S. Niemelä, Ilpo Vattulainen, Erik Lindahl
2008	—	`conf`	Architecture-aware design of a decimation filter based on a dual wordlength multiply-accumulate unit. ACSCC Erik Lindahl, Oscar Gustafsson
2008	J	`jnl`	Effect of Cobratoxin Binding on the Normal Mode Vibration within Acetylcholine Binding Protein. J. Chem. Inf. Model. Edward J. Bertaccini, Erik Lindahl, Titia Sixma, James R. Trudell
2007	A	`conf`	A multi-agent system of evidential reasoning for intelligence analyses. AAMAS Erik Lindahl, Stephen O'Hara, Qiuming Zhu
2007	J	`jnl`	Normal-Mode Analysis of the Glycine Alpha1 Receptor by Three Separate Methods. J. Chem. Inf. Model. Edward J. Bertaccini, James R. Trudell, Erik Lindahl
2007	J	`jnl`	Speeding up parallel GROMACS on high-latency networks. J. Comput. Chem. Carsten Kutzner, David van der Spoel, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. de Groot, Helmut Grubmüller
2006	—	`conf`	Improved GROMACS Scaling on Ethernet Switched Clusters. PVM/MPI Carsten Kutzner, David van der Spoel, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. de Groot, Helmut Grubmüller
2006	J	`jnl`	NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis. Nucleic Acids Res. Erik Lindahl, Cyril Azuara, Patrice Koehl, Marc Delarue
2006	J	`jnl`	PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics. Nucleic Acids Res. Cyril Azuara, Erik Lindahl, Patrice Koehl, Henri Orland, Marc Delarue
2005	J	`jnl`	GROMACS: Fast, flexible, and free. J. Comput. Chem. David van der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen