Leif A. Eriksson
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View article: Correction to “Computational Characterization of the Interaction of CARD Domains in the Apoptosome”
Correction to “Computational Characterization of the Interaction of CARD Domains in the Apoptosome” Open
View article: MolAI: A Deep Learning Framework for Data-Driven Molecular Descriptor Generation and Advanced Drug Discovery Applications
MolAI: A Deep Learning Framework for Data-Driven Molecular Descriptor Generation and Advanced Drug Discovery Applications Open
This study introduces MolAI, a robust deep learning model designed for data-driven molecular descriptor generation. Utilizing a vast training data set of 221 million unique compounds, MolAI employs an autoencoder neural machine translation…
View article: Discovery of a reversible ALDH1A3 inhibitor through a consensus docking-based virtual screening study
Discovery of a reversible ALDH1A3 inhibitor through a consensus docking-based virtual screening study Open
View article: In silico identification of substrate-binding sites in type-1A α-synuclein amyloids
In silico identification of substrate-binding sites in type-1A α-synuclein amyloids Open
Pathological amyloids associated with Parkinson and Alzheimer diseases have been shown to catalyze chemical reactions in vitro. To elucidate how small-molecule substrates interact with cross-β amyloid structures, we here employ computation…
View article: Combining kinetics and in silico approaches to evaluate bromhexine as an anti-pancreatic lipase agent for obesity management
Combining kinetics and in silico approaches to evaluate bromhexine as an anti-pancreatic lipase agent for obesity management Open
Industrialization, fast food intake and reduced physical activity, mainly in developed countries, exacerbate obesity and make it a major lifestyle disorder. A promising strategy for developing effective anti-obesity agents is to inhibit pa…
View article: Design of Computer Simulation Exercises on Polarity and Intermolecular Attractive Forces
Design of Computer Simulation Exercises on Polarity and Intermolecular Attractive Forces Open
View article: FMO4 drives lung adenocarcinoma by stabilizing the MAT2A/MAT2B complex and hindering ferroptosis
FMO4 drives lung adenocarcinoma by stabilizing the MAT2A/MAT2B complex and hindering ferroptosis Open
Lung cancer is the leading cause of death by cancer in the world and finding new targets is a major medical need to tackle this disease. Here, upon proteomic analysis to identify common players in oncogenic EGFR- and KRAS-driven lung adeno…
View article: MolAI: A Deep Learning Framework for Data-driven Molecular Descriptor Generation and Advanced Drug Discovery Applications
MolAI: A Deep Learning Framework for Data-driven Molecular Descriptor Generation and Advanced Drug Discovery Applications Open
This study introduces MolAI, a robust deep learning model designed for data-driven molecular descriptor generation. Utilizing a vast training dataset of 221 million unique compounds, MolAI employs an autoencoder neural machine translation …
View article: iScore: A ML-Based Scoring Function for De Novo Drug Discovery
iScore: A ML-Based Scoring Function for De Novo Drug Discovery Open
In the quest for accelerating de novo drug discovery, the development of efficient and accurate scoring functions represents a fundamental challenge. This study introduces iScore, a novel machine learning (ML)-based scoring function design…
View article: Unraveling the Binding Mode of TSC2–Rheb through Protein Docking and Simulations
Unraveling the Binding Mode of TSC2–Rheb through Protein Docking and Simulations Open
Proteasome inhibitors (PIs) constitute the first line of therapy for multiple myeloma (MM). Despite the impressive clinical efficacy, MM remains fatal due to the development of drug resistance over time. During MM progression, stress respo…
View article: Computational Characterization of the Interaction of CARD Domains in the Apoptosome
Computational Characterization of the Interaction of CARD Domains in the Apoptosome Open
The apoptosome, a critical protein complex in apoptosis regulation, relies on intricate interactions between its components, particularly the proteins containing the Caspase Activation and Recruitment Domain (CARD). This work presents a th…
View article: An experimental target-based platform in yeast for screening Plasmodium vivax deoxyhypusine synthase inhibitors
An experimental target-based platform in yeast for screening Plasmodium vivax deoxyhypusine synthase inhibitors Open
The enzyme deoxyhypusine synthase (DHS) catalyzes the first step in the post-translational modification of the eukaryotic translation factor 5A (eIF5A). This is the only protein known to contain the amino acid hypusine, which results from …
View article: Proximity Interactome analyses unveil novel regulators of IRE1α canonical signaling
Proximity Interactome analyses unveil novel regulators of IRE1α canonical signaling Open
The unfolded protein response (UPR) is a key adaptive pathway that controls endoplasmic reticulum (ER) homeostasis. The UPR is transduced by three ER-resident sensors of ER homeostasis disruption in the lumen of this compartment. They trig…
View article: Mechanism of Dual-Site Recognition in a Classic DNA Aptamer
Mechanism of Dual-Site Recognition in a Classic DNA Aptamer Open
Nucleic acid aptamers possess unique advantages in specific recognition. However, the lack of in-depth investigation into their dynamic recognition mechanisms has restricted their rational design and potential applications in fields such a…
View article: Selectivity analysis of diaminopyrimidine-based inhibitors of MTHFD1, MTHFD2 and MTHFD2L
Selectivity analysis of diaminopyrimidine-based inhibitors of MTHFD1, MTHFD2 and MTHFD2L Open
View article: An automated positive selection screen in yeast provides support for boron-containing compounds as inhibitors of SARS-CoV-2 main protease
An automated positive selection screen in yeast provides support for boron-containing compounds as inhibitors of SARS-CoV-2 main protease Open
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus continues to cause severe disease and deaths in many parts of the world, despite massive vaccination efforts. Antiviral drugs to curb an ongoing infection remain a prio…
View article: Phosphorylation of GCN2 by mTOR confers adaptation to conditions of hyper-mTOR activation under stress
Phosphorylation of GCN2 by mTOR confers adaptation to conditions of hyper-mTOR activation under stress Open
Adaptation to the shortage in free amino acids (AA) is mediated by 2 pathways, the integrated stress response (ISR) and the mechanistic target of rapamycin (mTOR). In response to reduced levels, primarily of leucine or arginine, mTOR in it…
View article: Selectivity analysis of diaminopyrimidine-based inhibitors of MTHFD1, MTHFD2 and MTHFD2L
Selectivity analysis of diaminopyrimidine-based inhibitors of MTHFD1, MTHFD2 and MTHFD2L Open
The mitochondrial enzyme methylenetetrahydrofolate dehydrogenase (MTHFD2) is involved in purine and thymidine synthesis via 1C metabolism. MTHFD2 is exclusively overexpressed in cancer cells but absent in most healthy adult human tissues. …
View article: iScore: A ML-Based Scoring Function for<i>de novo</i>Drug Discovery
iScore: A ML-Based Scoring Function for<i>de novo</i>Drug Discovery Open
In the quest for accelerating de novo drug discovery, the development of efficient and accurate scoring functions represents a fundamental challenge. This study introduces iScore, a novel machine learning (ML)-based scoring function design…
View article: Selective Bias Virtual Screening for Discovery of Promising Antimalarial Candidates targeting Plasmodium N-Myristoyltransferase
Selective Bias Virtual Screening for Discovery of Promising Antimalarial Candidates targeting Plasmodium N-Myristoyltransferase Open
Malaria remains a significant public health challenge, with Plasmodium vivax being the species responsible for the most prevalent form of the disease. Given the limited therapeutic options available, the search for new antimalarials agains…
View article: Multiscale <i>In Silico</i> Study of the Mechanism of Activation of the RtcB Ligase by the PTP1B Phosphatase
Multiscale <i>In Silico</i> Study of the Mechanism of Activation of the RtcB Ligase by the PTP1B Phosphatase Open
Inositol-requiring enzyme 1 (IRE1) is a transmembrane sensor that is part of a trio of sensors responsible for controlling the unfolded protein response within the endoplasmic reticulum (ER). Upon the accumulation of unfolded or misfolded …
View article: Different binding modalities of quercetin to inositol-requiring enzyme 1 of S. cerevisiae and human lead to opposite regulation
Different binding modalities of quercetin to inositol-requiring enzyme 1 of S. cerevisiae and human lead to opposite regulation Open
The flavonoid Quercetin (Qe) was identified as an activator of Inositol-requiring enzyme 1 (IRE1) in S. cerevisiae ( sc Ire1p), but its impact on human IRE1 ( h IRE1) remains controversial due to the absence of a conserved Qe binding site.…
View article: Dess–Martin periodinane-mediated oxidation of the primary alcohol of cytidine into a carboxylic acid
Dess–Martin periodinane-mediated oxidation of the primary alcohol of cytidine into a carboxylic acid Open
Herein we describe the first example of the conversion of the primary alcohol of cytidine into a carboxylic acid by use of the Dess–Martin periodinane oxidising agent.
View article: An experimental target-based platform in yeast for screening<i>Plasmodium vivax</i>deoxyhypusine synthase inhibitors
An experimental target-based platform in yeast for screening<i>Plasmodium vivax</i>deoxyhypusine synthase inhibitors Open
The enzyme deoxyhypusine synthase (DHS) catalyzes the first step in the post-translational modification of the eukaryotic translation factor 5A (eIF5A). This is the only protein known to contain the amino acid hypusine, which results from …
View article: Insights into the structure and function of the RNA ligase RtcB
Insights into the structure and function of the RNA ligase RtcB Open
To be functional, some RNAs require a processing step involving splicing events. Each splicing event necessitates an RNA ligation step. RNA ligation is a process that can be achieved with various intermediaries such as self-catalysing RNAs…
View article: UFMylation: a ubiquitin-like modification
UFMylation: a ubiquitin-like modification Open
View article: Improved Algorithms for Allen's Interval Algebra by Dynamic Programming with Sublinear Partitioning
Improved Algorithms for Allen's Interval Algebra by Dynamic Programming with Sublinear Partitioning Open
Allen's interval algebra is one of the most well-known calculi in qualitative temporal reasoning with numerous applications in artificial intelligence. Very recently, there has been a surge of improvements in the fine-grained complexity of…
View article: A Fast Algorithm for Consistency Checking Partially Ordered Time
A Fast Algorithm for Consistency Checking Partially Ordered Time Open
Partially ordered models of time occur naturally in applications where agents/processes cannot perfectly communicate with each other, and can be traced back to the seminal work of Lamport. In this paper we consider the problem of deciding …
View article: Dataset for Multiscale in silico study of mechanism of activation of RtcB ligase by PTP1B phosphatase.
Dataset for Multiscale in silico study of mechanism of activation of RtcB ligase by PTP1B phosphatase. Open
The pdb structures of the RtcB_PTP1B complex after protein-protein docking and after 1000ns MD simulation, 1000ns MD trajectory, and a video captured from the QM/MM WT-MetaD simulation trajectory showing the reaction mechanism
View article: Dataset for Multiscale in silico study of mechanism of activation of RtcB ligase by PTP1B phosphatase.
Dataset for Multiscale in silico study of mechanism of activation of RtcB ligase by PTP1B phosphatase. Open
The pdb structures of the RtcB_PTP1B complex after protein-protein docking and after 1000ns MD simulation, 1000ns MD trajectory, and a video captured from the QM/MM WT-MetaD simulation trajectory showing the reaction mechanism