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List of works by Anders Wallqvist

2D SMARTCyp reactivity-based site of metabolism prediction for major drug-metabolizing cytochrome P450 enzymes

scientific article published on 4 June 2012

3-substituted indole inhibitors against Francisella tularensis FabI identified by structure-based virtual screening

scientific article published on July 2013

A Model for Studying Drying at Hydrophobic Interfaces: Structural and Thermodynamic Properties†

scientific article published in July 2001

A Reaction Path Study of the Catalysis and Inhibition of the Bacillus anthracis CapD γ-Glutamyl Transpeptidase

scientific article published on 31 October 2014

A Web-Accessible Protein Structure Prediction Pipeline

scientific article published in June 2009

A computational study of the respiratory airflow characteristics in normal and obstructed human airways

scientific article published on 25 June 2014

A fusion-inhibiting peptide against Rift Valley fever virus inhibits multiple, diverse viruses

scientific article published on 12 September 2013

A mevalonate bypass system facilitates elucidation of plastid biology in malaria parasites

scientific article published on 14 February 2020

A molecular dynamics study of polarizable water

scientific article published on 20 October 1989

A novel scoring approach for protein co-purification data reveals high interaction specificity

scientific article

A physicochemical descriptor-based scoring scheme for effective and rapid filtering of kinase-like chemical space

scientific article published on 8 February 2012

A reverse-phase protein microarray-based screen identifies host signaling dynamics upon Burkholderia spp. infection

scientific article

A simplified metabolic network reconstruction to promote understanding and development of flux balance analysis tools

scientific article published in February 2019

A strategy for evaluating pathway analysis methods.

scientific article published on 13 October 2017

A systems biology framework for modeling metabolic enzyme inhibition of Mycobacterium tuberculosis

scientific article published on 15 September 2009

A systems biology strategy to identify molecular mechanisms of action and protein indicators of traumatic brain injury

scientific article published on 14 November 2014

An Integrated Docking Pipeline for the Prediction of Large-Scale Protein-Protein Interactions

scientific article published in June 2010

Analysis of protein-protein interactions and the effects of amino acid mutations on their energetics. The importance of water molecules in the binding epitope

scientific article published in June 1997

Anticancer medicines in development: assessment of bioactivity profiles within the National Cancer Institute anticancer screening data

scientific article published in August 2007

Anticancer metal compounds in NCI's tumor-screening database: putative mode of action

scientific article published in April 2005

Assessing Airflow Sensitivity to Healthy and Diseased Lung Conditions in a Computational Fluid Dynamics Model Validated In Vitro

scientific article published on 5 January 2018

Assessing Chemical-Induced Liver Injury In Vivo From In Vitro Gene Expression Data in the Rat: The Case of Thioacetamide Toxicity

scientific article published on 26 November 2019

Assessing deep and shallow learning methods for quantitative prediction of acute chemical toxicity.

scientific article published on 2 May 2018

Assessment of in vitro and in vivo activities in the National Cancer Institute's anticancer screen with respect to chemical structure, target specificity, and mechanism of action

scientific article published on March 2006

Azodicarbonamide inhibits HIV-1 replication by targeting the nucleocapsid protein.

scientific article

BRILIA: Integrated Tool for High-Throughput Annotation and Lineage Tree Assembly of B-Cell Repertoires

scientific article published on January 2016

Biofilm Formation Mechanisms of Pseudomonas aeruginosa Predicted via Genome-Scale Kinetic Models of Bacterial Metabolism

scientific article

Bioinformatic analysis of patient-derived ASPS gene expressions and ASPL-TFE3 fusion transcript levels identify potential therapeutic targets

scientific article

Bridging the gap between gene expression and metabolic phenotype via kinetic models

scientific article published on 22 July 2013

Can computationally designed protein sequences improve secondary structure prediction?

scientific article published on 31 January 2011

Categorizing biases in high-confidence high-throughput protein-protein interaction data sets

scientific article

Characterization of chemically induced liver injuries using gene co-expression modules

scientific article

Chemoinformatic analysis of NCI preclinical tumor data: evaluating compound efficacy from mouse xenograft data, NCI-60 screening data, and compound descriptors

scientific article published on 8 June 2007

Classification of scaffold-hopping approaches

scientific article published on 26 October 2011

Combinatorial peptide-based epitope mapping from Ebola virus DNA vaccines and infections reveals residue-level determinants of antibody binding

scientific article published on 18 September 2017

Comparative Proteomic Analysis of Liver Steatosis and Fibrosis after Oral Hepatotoxicant Administration in Sprague-Dawley Rats

scientific article published in January 2018

Comprehensive analysis of pathway or functionally related gene expression in the National Cancer Institute's anticancer screen

scientific article published on 04 January 2006

Computational Approach To Characterize Causative Factors and Molecular Indicators of Chronic Wound Inflammation

scientific article published on 22 January 2014

Computational and experimental validation of B and T-cell epitopes of the in vivo immune response to a novel malarial antigen

scientific article

Computational tools and resources for metabolism-related property predictions. 1. Overview of publicly available (free and commercial) databases and software

scientific article (publication date: October 2012)

Computer Simulations of Type I Gas Hydrates in the Presence of Methanol

scientific article published in April 1994

Computing Relative Free Energies of Solvation using Single Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange

scientific article published in November 2010

Conceptual Model of Biofilm Antibiotic Tolerance That Integrates Phenomena of Diffusion, Metabolism, Gene Expression, and Physiology

scientific article published on 21 October 2019

Concordance between Thioacetamide-Induced Liver Injury in Rat and Human In Vitro Gene Expression Data

scientific article published on 04 June 2020

Cooperative folding units of escherichia coli tryptophan repressor.

scientific article

Correlation between Native-State Hydrogen Exchange and Cooperative Residue Fluctuations from a Simple Model ⬇️

scientific article published on January 27, 1998

Critically Assessing the Predictive Power of QSAR Models for Human Liver Microsomal Stability

scientific article published on 14 July 2015

DBSecSys 2.0: a database of Burkholderia mallei and Burkholderia pseudomallei secretion systems

scientific article published on 20 September 2016

DBSecSys: a database of Burkholderia mallei secretion systems.

scientific article published on 16 July 2014

DOVIS 2.0: an efficient and easy to use parallel virtual screening tool based on AutoDock 4.0.

scientific article published on 8 September 2008

DOVIS: an implementation for high-throughput virtual screening using AutoDock

scientific article published on 27 February 2008

Data-driven identification of structural alerts for mitigating the risk of drug-induced human liver injuries

scientific article (publication date: 2015)

Data-driven prediction of adverse drug reactions induced by drug-drug interactions.

scientific article published on 8 June 2017

Deep Neural Network Models for Predicting Chemically Induced Liver Toxicity Endpoints From Transcriptomic Responses

article

Delayed fractional dose regimen of the RTS,S/AS01 malaria vaccine candidate enhances an IgG4 response that inhibits serum opsonophagocytosis

scientific article published on 11 August 2017

Dengue virus antibody database: Systematically linking serotype-specificity with epitope mapping in dengue virus

scientific article published on 21 February 2017

Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis

scientific article published on 23 November 2010

Differential gene expression as a potential classifier of 2-(4-amino-3-methylphenyl)-5-fluorobenzothiazole-sensitive and -insensitive cell lines

scientific article published on 6 December 2005

Dissecting Machine-Learning Prediction of Molecular Activity: Is an Applicability Domain Needed for Quantitative Structure–Activity Relationship Models Based on Deep Neural Networks?

scientific article published on 9 November 2018

Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the Surface Generalized Born solvent model

article

Drugs aimed at targeting characteristic karyotypic phenotypes of cancer cells

scientific article published on October 2005

Efficient Conformational Sampling in Explicit Solvent Using a Hybrid Replica Exchange Molecular Dynamics Method

scientific article published on 3 February 2012

Enabling data-limited chemical bioactivity predictions through deep neural network transfer learning

scientific article published in 2022

Epitope mapping of Ebola virus dominant and subdominant glycoprotein epitopes facilitates construction of an epitope-based DNA vaccine able to focus the antibody response in mice

scientific article published on 12 July 2017

Evaluating chemical structure similarity as an indicator of cellular growth inhibition

scientific article published in January 2006

Evidence of probabilistic behaviour in protein interaction networks

scientific article

Ewald summation retards translational motion in molecular dynamics simulation of water

scientific article published on 20 January 1992

Ewald summation retards translational motion in molecular dynamics simulation of water

scientific article published on 17 March 1990

Exploiting large-scale drug-protein interaction information for computational drug repurposing

scientific article

Exploring chemical reaction mechanisms through harmonic Fourier beads path optimization

scientific article published in October 2013

Exploring polypharmacology using a ROCS-based target fishing approach

scientific article published on 23 January 2012

FIEFDom: a transparent domain boundary recognition system using a fuzzy mean operator

scientific article published in February 2009

Free Energy Difference in Indolicidin Attraction to Eukaryotic and Prokaryotic Model Cell Membranes

scientific article published on 29 February 2012

Free-energy profiles of membrane insertion of the M2 transmembrane peptide from influenza A virus

scientific article published on August 2008

Fungal bis-Naphthopyrones as Inhibitors of Botulinum Neurotoxin Serotype A.

scientific article published on 2 April 2012

Gene Expression Patterns Associated With Histopathology in Toxic Liver Fibrosis.

scientific article published on 22 September 2015

General Approach to Estimate Error Bars for Quantitative Structure–Activity Relationship Predictions of Molecular Activity

scientific article published on 27 June 2018

General Purpose 2D and 3D Similarity Approach to Identify hERG Blockers

scientific article published on 30 December 2015

Genome-Scale Model-Based Identification of Metabolite Indicators for Early Detection of Kidney Toxicity

scientific article published on 01 February 2020

Genome-wide gene expression changes associated with exposure of rat liver, heart, and kidney cells to endosulfan

scientific article published on 29 January 2018

Identification of the Toxicity Pathways Associated With Thioacetamide-Induced Injuries in Rat Liver and Kidney

scientific article published in 2018

Identifying cytochrome p450 functional networks and their allosteric regulatory elements

scientific article (publication date: 2013)

Identifying metabolic adaptations characteristic of cardiotoxicity using paired transcriptomics and metabolomics data integrated with a computational model of heart metabolism

scientific article published on 29 February 2024

Improved Binding Free Energy Predictions from Single-Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange

scientific article published in September 2011

In silico analyses of substrate interactions with human serum paraoxonase 1.

scientific article published in May 2009

Incorporating intramolecular degrees of freedom in simulations of polarizable liquid water

scientific article published in December 1990

Inferring high-confidence human protein-protein interactions ⬇️

scientific article published on May 4, 2012

Influence of protein abundance on high-throughput protein-protein interaction detection

scientific article

Inter-study and time-dependent variability of metabolite abundance in cultured red blood cells

scientific article published on 2 July 2021

Interaction of the disordered Yersinia effector protein YopE with its cognate chaperone SycE.

scientific article published on December 2009

Intermolecular Potential Variation due to Intramolecular Rotation in Molecules

scientific article published in July 1991

Linking pathway gene expressions to the growth inhibition response from the National Cancer Institute's anticancer screen and drug mechanism of action.

scientific article published on January 2005

Linking the growth inhibition response from the National Cancer Institute's anticancer screen to gene expression levels and other molecular target data

scientific article published in November 2003

Linking tumor cell cytotoxicity to mechanism of drug action: an integrated analysis of gene expression, small-molecule screening and structural databases

scientific article published in May 2005

Locally weighted learning methods for predicting dose-dependent toxicity with application to the human maximum recommended daily dose

scientific article published on 26 September 2012

Mechanisms of action of Coxiella burnetii effectors inferred from host-pathogen protein interactions

scientific article published on 27 November 2017

Mechanistic identification of biofluid metabolite changes as markers of acetaminophen-induced liver toxicity in rats

scientific article published on 08 April 2019

Membrane Insertion Profiles of Peptides Probed by Molecular Dynamics Simulations

scientific article published in 2008

Merging applicability domains for in silico assessment of chemical mutagenicity

scientific article published on 14 February 2014

Metabolic Survival Adaptations of Plasmodium falciparum Exposed to Sublethal Doses of Fosmidomycin

scientific article published on 18 March 2021

Metabolic adjustments of blood-stage Plasmodium falciparum in response to sublethal pyrazoleamide exposure

scientific article published on 21 January 2022

Metabolic alterations in the erythrocyte during blood-stage development of the malaria parasite

scientific article published on 27 February 2020

Metabolic host responses to malarial infection during the intraerythrocytic developmental cycle

scientific article

Metabolic network-based predictions of toxicant-induced metabolite changes in the laboratory rat

scientific article published in Scientific Reports

Mining Public Toxicogenomic Data Reveals Insights and Challenges in Delineating Liver Steatosis Adverse Outcome Pathways

scientific article published on 18 October 2019

Mining host-pathogen protein interactions to characterize Burkholderia mallei infectivity mechanisms.

scientific article

Mining kidney toxicogenomic data by using gene co-expression modules

scientific article (publication date: 10 October 2016)

Modeling metabolism and stage-specific growth of Plasmodium falciparum HB3 during the intraerythrocytic developmental cycle

scientific article published in October 2014

Modeling phenotypic metabolic adaptations of Mycobacterium tuberculosis H37Rv under hypoxia

scientific article

Modeling synergistic drug inhibition of Mycobacterium tuberculosis growth in murine macrophages

scientific article published in 2011

Modeling the Role of Epitope Arrangement on Antibody Binding Stoichiometry in Flaviviruses

scientific article published on October 2016

Molecular Similarity-Based Domain Applicability Metric Efficiently Identifies Out-of-Domain Compounds

scientific article published on 7 November 2018

Molecular Simulations Reveal the Role of Antibody Fine Specificity and Viral Maturation State on Antibody-Dependent Enhancement of Infection in Dengue Virus

scientific article published in 2019

Molecular Structure-Based Large-Scale Prediction of Chemical-Induced Gene Expression Changes.

scientific article published on 10 August 2017

Molecular dynamics study of hydrophobic aggregation in water/methane/methanol systems

scientific article published in August 1991

Network Modeling of Liver Metabolism to Predict Plasma Metabolite Changes During Short-Term Fasting in the Laboratory Rat

scientific article published on 01 March 2019

Neuroprotective mechanisms activated in non-seizing rats exposed to sarin

scientific article published on 4 June 2015

Nonequilibrium Phase Transitions Associated with DNA Replication

scientific article published on 9 February 2011

Nonyloxytryptamine mimics polysialic acid and modulates neuronal and glial functions in cell culture

scientific article published on 23 September 2013

Novel Burkholderia mallei virulence factors linked to specific host-pathogen protein interactions.

scientific article published on 24 June 2013

Novel plant-derived recombinant human interferons with broad spectrum antiviral activity

scientific article published on 14 October 2011

Obstructions in the lower airways lead to altered airflow patterns in the central airway

scientific article published on 01 October 2019

On the Implementation of Friedman Boundary Conditions in Liquid Water Simulations

scientific article published in April 1993

On the proper calculation of electrostatic interactions in solid-supported bilayer systems

scientific article published on 7 February 2011

PSPP: a protein structure prediction pipeline for computing clusters

scientific article published on 16 July 2009

PathNet: a tool for pathway analysis using topological information

scientific article published on 24 September 2012

Phenotypic Characterization of a Novel Virulence-Factor Deletion Strain of Burkholderia mallei That Provides Partial Protection against Inhalational Glanders in Mice

scientific article published on 26 February 2016

Polarizable water at a hydrophobic wall

scientific article published in January 1990

Predicting Rat and Human Pregnane X Receptor Activators Using Bayesian Classification Models

scientific article published on 7 September 2016

Prediction of metabolic flux distribution from gene expression data based on the flux minimization principle

scientific article

Probing the donor and acceptor substrate specificity of the γ-glutamyl transpeptidase

scientific article published on 2 February 2012

Probing the extent of randomness in protein interaction networks

scientific article (publication date: 2008)

QSAR classification model for antibacterial compounds and its use in virtual screening

scientific article

Quantitative Analysis of Repertoire-Scale Immunoglobulin Properties in Vaccine-Induced B-Cell Responses

scientific article published on 14 August 2017

Quantitative predictions of binding free energy changes in drug-resistant influenza neuraminidase

scientific article

Rapid countermeasure discovery against Francisella tularensis based on a metabolic network reconstruction

scientific article published in 2013

Reconciled rat and human metabolic networks for comparative toxicogenomics and biomarker predictions

scientific article

Reconstituting protein interaction networks using parameter-dependent domain-domain interactions

scientific article published on 7 May 2013

Separation of Betti Reaction Product Enantiomers: Absolute Configuration and Inhibition of Botulinum Neurotoxin A

scientific article published on March 2011

Short-term metabolic adjustments in Plasmodium falciparum counter hypoxanthine deprivation at the expense of long-term viability

scientific article published on 19 March 2019

Simulation of B cell affinity maturation explains enhanced antibody cross-reactivity induced by the polyvalent malaria vaccine AMA1.

scientific article published on 30 July 2014

Spontaneous Buckling of Lipid Bilayer and Vesicle Budding Induced by Antimicrobial Peptide Magainin 2: A Coarse-Grained Simulation Study

scientific article published on 30 June 2011

Structural investigation of C4b-binding protein by molecular modeling: localization of putative binding sites.

scientific article published in June 1998

Structure and Dynamics of End-to-End Loop Formation of the Penta-Peptide Cys-Ala-Gly-Gln-Trp in Implicit Solvents

scientific article published on 10 September 2009

Structure-based pKa prediction provides a thermodynamic basis for the role of histidines in pH-induced conformational transitions in dengue virus

scientific article published on 31 October 2015

Synthesis and biological properties of novel pyridinioalkanoyl thiolesters (PATE) as anti-HIV-1 agents that target the viral nucleocapsid protein zinc fingers.

scientific article published on January 1999

Synthesis and evaluation of Strychnos alkaloids as MDR reversal agents for cancer cell eradication

scientific article published on 21 December 2013

Systems level analysis and identification of pathways and networks associated with liver fibrosis

scientific article

Systems toxicology of chemically induced liver and kidney injuries: histopathology-associated gene co-expression modules

scientific article published in September 2016

Targeting changes in cancer: assessing pathway stability by comparing pathway gene expression coherence levels in tumor and normal tissues

scientific article published in September 2006

Teaching an Old Dog New Tricks: Strategies That Improve Early Recognition in Similarity-Based Virtual Screening

scientific article published on 23 October 2019

Ten simple rules on how to create open access and reproducible molecular simulations of biological systems

scientific article published in January 2019

The C4b-binding protein–protein S interaction is hydrophobic in nature

scientific article published in October 1998

The biological function of antibodies induced by the RTS,S/AS01 malaria vaccine candidate is determined by their fine specificity

scientific article published on 31 May 2016

Toxicant-Induced Metabolic Alterations in Lipid and Amino Acid Pathways Are Predictive of Acute Liver Toxicity in Rats

scientific article published on 04 November 2020

Unraveling the conundrum of seemingly discordant protein-protein interaction datasets

scientific article published in January 2010

Using Chemical-Induced Gene Expression in Cultured Human Cells to Predict Chemical Toxicity

scientific article published on 21 October 2016

Using a genome-scale metabolic network model to elucidate the mechanism of chloroquine action in Plasmodium falciparum

scientific article published on 22 March 2017

Using host-pathogen protein interactions to identify and characterize Francisella tularensis virulence factors

scientific article published on 29 December 2015

Using the Variable-Nearest Neighbor Method To Identify P-Glycoprotein Substrates and Inhibitors.

scientific article published on 16 November 2016

Using the antibody-antigen binding interface to train image-based deep neural networks for antibody-epitope classification

scientific article published on 29 March 2021

Vinorelbine and epirubicin share common features with polysialic acid and modulate neuronal and glial functions

scientific article published on 07 October 2015

Volumetric characteristics of idiopathic pulmonary fibrosis lungs: computational analyses of high-resolution computed tomography images of lung lobes

scientific article published on 11 October 2019

vNN Web Server for ADMET Predictions

scientific article published on 4 December 2017

β-Aminoalcohols as Potential Reactivators of Aged Sarin-/Soman-Inhibited Acetylcholinesterase

scientific article published on 13 February 2017

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