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Adaptive iterative retrieval for enhanced retrieval-augmented generation Open

Wenhan Han, Eric Jakobsson, Jun Wang, Mykola Pechenizkiy, Meng Fang · 2025

Dipole orientation of hydrated gas phase proteins Open

Harald Agelii, Eric Jakobsson, Emiliano De Santis, Gideon Elfrink, Thomas Mandl , et al. · 2025

We compare dehydrated with hydrated proteins in external electric fields in vacuum. Hydration reduces the required field strength for dipole orientation, makes the molecule orient at shorter time scales, and increases structural stability.

A Generalised Theory of Interactions -- II. The Theoretical Construction Open

Santiago Núñez-Corrales, Eric Jakobsson · 2024

After discussing the significance of interactions to understand complex multiscale stochastic systems (CMSS), we turn our attention to the construction of a Generalised Theory of Interactions (GToI). We define interactions as discrete, loc…

A Generalized Theory of Interactions -- I. The General Problem Open

Santiago Núñez-Corrales, Eric Jakobsson · 2024

Understanding realistic complex systems requires confronting significant conceptual, theoretical and experimental limitations rooted in the persistence of views that originated in the mechanics of simple moving bodies. We define the catego…

High-Dimensional Parameter Search Method to Determine Force Field Mixing Terms in Molecular Simulations Open

Matthew Saunders, Vered Wineman‐Fisher, Eric Jakobsson, Sameer Varma, Sagar Pandit · 2022

Molecular dynamics (MD) force fields for lipids and ions are typically developed independently of one another. In simulations consisting of both lipids and ions, lipid-ion interaction energies are estimated using a predefined set of mixing…

ResidueFinder: extracting individual residue mentions from protein literature Open

Ton E Becker, Eric Jakobsson · 2021

Additional file 5 of ResidueFinder: extracting individual residue mentions from protein literature Open

Ton E Becker, Eric Jakobsson · 2021

Part of archive containing the regexes used and analyzed in this study. This part of the archive is the full version 1 RF regex. It is also in the SourceForge web site.

Additional file 6 of ResidueFinder: extracting individual residue mentions from protein literature Open

Ton E Becker, Eric Jakobsson · 2021

Part of archive containing the regexes used and analyzed in this study. This part of the archive is the cut version of the version 1 regex. It is also in the SourceForge web site.

Additional file 10 of ResidueFinder: extracting individual residue mentions from protein literature Open

Ton E Becker, Eric Jakobsson · 2021

Part of archive containing the regexes used and analyzed in this study. This part of the archive is the cut version of the version 3 regex. It is also in the SourceForge web site.

Additional file 4 of ResidueFinder: extracting individual residue mentions from protein literature Open

Ton E Becker, Eric Jakobsson · 2021

Part of archive containing the regexes used and analyzed in this study. This part of the archive is the cut version of the MutationFinder regex. It is also in the SourceForge web site.

Additional file 3 of ResidueFinder: extracting individual residue mentions from protein literature Open

Ton E Becker, Eric Jakobsson · 2021

Part of archive containing the regexes used and analyzed in this study. This part of the archive is the MutationFinder regex. It is also in the SourceForge web site.

Additional file 2 of ResidueFinder: extracting individual residue mentions from protein literature Open

Ton E Becker, Eric Jakobsson · 2021

Computed Performance Data. This spreadsheet directly shows the numbers underlying the tables presented in the manuscript, including the PMID’s for documents analyzed.

Additional file 9 of ResidueFinder: extracting individual residue mentions from protein literature Open

Ton E Becker, Eric Jakobsson · 2021

Part of archive containing the regexes used and analyzed in this study. This part of the archive is the full version 3 RF regex. It is also in the SourceForge web site.

Additional file 8 of ResidueFinder: extracting individual residue mentions from protein literature Open

Ton E Becker, Eric Jakobsson · 2021

Part of archive containing the regexes used and analyzed in this study. This part of the archive is the cut version of the version 2 regex. It is also in the SourceForge web site.

Additional file 7 of ResidueFinder: extracting individual residue mentions from protein literature Open

Ton E Becker, Eric Jakobsson · 2021

Part of archive containing the regexes used and analyzed in this study. This part of the archive is the full version 2 RF regex. It is also in the SourceForge web site.

Transferable interactions of Li+ and Mg2+ ions in polarizable models Open

Vered Wineman‐Fisher, Julián M. Delgado, Péter R. Nagy, Eric Jakobsson, Sagar A. Pandit , et al. · 2020

Therapeutic implications of Li+, in many cases, stem from its ability to inhibit certain Mg2+-dependent enzymes, where it interacts with or substitutes for Mg2+. The underlying details of its action are, however, unknown. Molecular simulat…

The Epidemiology Workbench: a Tool for Communities to Strategize in Response to COVID-19 and other Infectious Diseases Open

Santiago Núñez-Corrales, Eric Jakobsson · 2020

COVID-19 poses a dramatic challenge to health, community life, and the economy of communities across the world. While the properties of the virus are similar from place to place, the impact has been dramatically different from place to pla…

Computational Recipe for Designing Antibodies against the Ebola Virus Open

Amir Barati Farimani, N. R. Aluru, Emad Tajkhorshid, Eric Jakobsson · 2020

A conceptual basis for antiviral therapy is to deliver a synthetic antibody that binds to a viral surface protein, and thus prevents the virus from deploying its cell-entry mechanism. The fast and untraceable virus mutations take lives of …

Combining Physics-Based and Evolution-Based Methods to Design Antibodies Against an Evolving Virus Open

Eric Jakobsson, Amir Barati Farimani, Emad Tajkhorshid, N. R. Aluru · 2020

Undersökning av möjligheten till utveckling av kommersiellt tillgänglig koldioxidlagring i Sverige Open

Eric Jakobsson · 2020

Jordens befolkning behöver kraftigt reducera koldioxidutsläppen till atmosfären för att förhindra klimatförändringar. Klimatmål har sats upp av unioner och länder där de bland annat vill förhindra en global temperaturökning över 1.5 grader…

Systems Biology Understanding of the Effects of Lithium on Cancer Open

Weihao Ge, Eric Jakobsson · 2019

Lithium has many widely varying biochemical and phenomenological effects, suggesting that a systems biology approach is required to understand its action. Multiple lines of evidence point to lithium as a significant factor in development o…

Using Optimal F-Measure and Random Resampling in Gene Ontology Enrichment Calculations Open

Weihao Ge, Zeeshan Fazal, Eric Jakobsson · 2019

Background: A central question in bioinformatics is how to minimize arbitrariness and bias in analysis of patterns of enrichment in data. A prime example of such a question is enrichment of gene ontology (GO) classes in lists of genes. Our…

Rationally designing antisense therapy to keep up with evolving bacterial resistance Open

Seyfullah Kotil, Eric Jakobsson · 2019

Antisense molecules used as antibiotics offer the potential to keep up with acquired resistance, by redesigning the sequence of an antisense. Once bacteria acquire resistance by mutating the targeted sequence, new antisense can readily be …

Systems Biology Understanding of the Effects of Lithium on Affective and Neurodegenerative Disorders Open

Weihao Ge, Eric Jakobsson · 2018

Lithium has many widely varying biochemical and phenomenological effects, suggesting that a systems biology approach is required to understand its action. Multiple lines of evidence point to lithium intake and consequent blood levels as im…

An assessment of true and false positive detection rates of stepwise epistatic model selection as a function of sample size and number of markers Open

Angela H. Chen, Weihao Ge, William W. Metcalf, Eric Jakobsson, Liudmila S. Mainzer , et al. · 2018

Systems Biology Understanding of the Effects of Lithium on Cancer Open

Weihao Ge, Eric Jakobsson · 2018

Lithium has many widely varying biochemical and phenomenological effects, suggesting that a systems biology approach is required to understand its action. Multiple lines of evidence point to lithium as a significant factor in development o…

Using Optimal F-Measure and Random Resampling in Gene Ontology Enrichment Calculations Open

Weihao Ge, Zeeshan Fazal, Eric Jakobsson · 2017

Background A central question in bioinformatics is how to minimize arbitrariness and bias in analysis of patterns of enrichment in data. A prime example of such a question is enrichment of gene ontology (GO) classes in lists of genes. Our …

Towards a Unified Understanding of Lithium Action in Basic Biology and its Significance for Applied Biology Open

Eric Jakobsson, Orlando Argüello‐Miranda, See-Wing Chiu, Zeeshan Fazal, James Kruczek , et al. · 2017

Unique Modification of Membrane Structure by Lithium: A Molecular Dynamics Study Open

James Kruczek, See-Wing Chiu, Eric Jakobsson, Sagar A. Pandit · 2017

Fourier Analysis of Conservation Patterns in Protein Secondary Structure Open

Ashok Palaniappan, Eric Jakobsson · 2017

Residue conservation is a common observation in alignments of protein families, underscoring positions important in protein structure and function. Though many methods measure the level of conservation of particular residue positions, curr…

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