A. Wallqvist

发表

Mining the NCI screening database: explorations of agents involved in cell cycle regulation.

D. Covell, A. Monks, R. Shoemaker, 2003, Progress in cell cycle research.

Simplified amino acid alphabets for protein fold recognition and implications for folding.

R. Levy, A. Wallqvist, L. Murphy, 2000, Protein engineering.

Influence of Protein Abundance on High-Throughput Protein-Protein Interaction Detection

J. Reifman, A. Wallqvist, J. Ivanic, 2009, PloS one.

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

Ruifeng Liu, Anders Wallqvist, Hao Wang, 2019, Front. Pharmacol..

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

D. Covell, A. Wallqvist, N. Thanki, 2005, The Pharmacogenomics Journal.

A preference‐based free‐energy parameterization of enzyme‐inhibitor binding. Applications to HIV‐1‐protease inhibitor design

R L Jernigan, D. Covell, R. Jernigan, 1995, Protein science : a publication of the Protein Society.

Computational and Experimental Validation of B and T-Cell Epitopes of the In Vivo Immune Response to a Novel Malarial Antigen

V. DelVecchio, A. Wallqvist, S. Chaudhury, 2013, PloS one.

A Fusion-Inhibiting Peptide against Rift Valley Fever Virus Inhibits Multiple, Diverse Viruses

Anders Wallqvist, Daniel R. Ripoll, Jeffrey W. Koehler, 2013, PLoS neglected tropical diseases.

HYDROPHOBIC INTERACTIONS IN AQUEOUS UREA SOLUTIONS WITH IMPLICATIONS FOR THE MECHANISM OF PROTEIN DENATURATION

Anders Wallqvist, David G. Covell, D. Thirumalai, 1998 .

INVESTIGATION OF THE TEMPERATURE DEPENDENCE OF DIELECTRIC RELAXATION IN LIQUID WATER BY THZ REFLECTION SPECTROSCOPY AND MOLECULAR DYNAMICS SIMULATION

So, K. Mikkelsen, P. Åstrand, 1997 .

Systems Level Analysis and Identification of Pathways and Networks Associated with Liver Fibrosis

Jonathan D. Stallings, A. Wallqvist, D. Ippolito, 2014, PloS one.

Molecular classification of cancer: unsupervised self-organizing map analysis of gene expression microarray data.

D. Covell, A. Wallqvist, A. Rabow, 2003, Molecular cancer therapeutics.

Prediction of Metabolic Flux Distribution from Gene Expression Data Based on the Flux Minimization Principle

J. Reifman, A. Wallqvist, Hyun‐Seob Song, 2014, PloS one.

Correlation between native-state hydrogen exchange and cooperative residue fluctuations from a simple model.

D. Covell, R. Jernigan, I. Bahar, 1998, Biochemistry.

A simplified amino acid potential for use in structure predictions of proteins

A. Wallqvist, M. Ullner, 1994, Proteins.

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

J. Reifman, A. Wallqvist, S. Prigge, 2017, International journal for parasitology. Drugs and drug resistance.

Categorizing Biases in High-Confidence High-Throughput Protein-Protein Interaction Data Sets*

Jaques Reifman, Anders Wallqvist, Vesna Memišević, 2011, Molecular & Cellular Proteomics.

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

A. Wallqvist, N. Waters, S. Chaudhury, 2017, Scientific Reports.

Gene Expression Patterns Associated With Histopathology in Toxic Liver Fibrosis.

Anders Wallqvist, Jonathan D. Stallings, A. Wallqvist, 2016, Toxicological sciences : an official journal of the Society of Toxicology.

Classification of scaffold-hopping approaches.

Anders Wallqvist, Hongmao Sun, Gregory Tawa, 2012, Drug discovery today.

Docking enzyme‐inhibitor complexes using a preference‐based free‐energy surface

D. Covell, A. Wallqvist, D G Covell, 1996, Proteins.

PSPP: A Protein Structure Prediction Pipeline for Computing Clusters

Jaques Reifman, Valmik Desai, Nela Zavaljevski, 2009, PloS one.

Identifying functional metabolic shifts in heart failure with the integration of omics data and a cardiomyocyte-specific, genome-scale model

Jason A. Papin, Kristopher D. Rawls, Bonnie V. Dougherty, 2020, bioRxiv.

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

Venkat R. Pannala, Jamey D. Young, J. Reifman, 2018, Scientific Reports.

Establishing connections between microarray expression data and chemotherapeutic cancer pharmacology.

Anders Wallqvist, E. Sausville, D. Covell, 2002, Molecular cancer therapeutics.

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

Venkat R. Pannala, Jamey D. Young, J. Reifman, 2020, International journal of molecular sciences.

Mechanism-based identification of plasma metabolites associated with liver toxicity.

Venkat R. Pannala, Jamey D. Young, J. Reifman, 2020, Toxicology.

Technology Review Special FocuS: compuTaTional chemiSTRy

Megan L. Peach, A. Zakharov, A. Wallqvist, 2012 .

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

J. Reifman, A. Wallqvist, L. Flors, 2019, Respiratory Research.

Scaffold-hopping provides both a conceptual and practical route for generating new lead series and chemistries with improved efficacy and pharmacokinetic properties based on known drugs and drug-target interactions.

A. Wallqvist, Hongmao Sun, G. Tawa, 2011 .

Spontaneous buckling of lipid bilayer and vesicle budding induced by antimicrobial peptide magainin 2: a coarse-grained simulation study.

Anders Wallqvist, A. Wallqvist, H. Woo, 2011, The journal of physical chemistry. B.

Drugs aimed at targeting characteristic karyotypic phenotypes of cancer cells

Ruili Huang, Anders Wallqvist, D. Covell, 2005, Molecular Cancer Therapeutics.

A molecular dynamics study of polarizable water

Anders Wallqvist, Bo Jönsson, Peter Ahlström, 1989 .

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

A. Wallqvist, Xin Hu, Kelly L. Robertson, 2012, Biochemistry.

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

Jaques Reifman, Ruifeng Liu, Anders Wallqvist, 2017, BMC Pharmacology and Toxicology.

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

J. Reifman, A. Wallqvist, S. Prigge, 2019, Malaria Journal.

A Toxicogenomic Approach to Assess Kidney Injury Induced by Mercuric Chloride in Rats.

A. Wallqvist, R. Printz, Patric Schyman, 2020, Toxicology.

Genome-Scale Characterization of Toxicity-Induced Metabolic Alterations in Primary Hepatocytes

Jason A. Papin, Kristopher D. Rawls, Venkat R. Pannala, 2019, Toxicological sciences : an official journal of the Society of Toxicology.

In vivo dynamics of the tracheal airway and its influences on respiratory airflows.

J. Reifman, A. Wallqvist, T. Altes, 2019, Journal of biomechanical engineering.

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

Venkat R. Pannala, A. Wallqvist, M. AbdulHameed, 2019, Front. Genet..

Topological Studies of the Amino Terminal Modules of Vitamin K-dependent Protein S Using Monoclonal Antibody Epitope Mapping and Molecular Modeling

A. Wallqvist, B. Dahlbäck, B. Villoutreix, 1998, Thrombosis and Haemostasis.

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

Michael S. Lee, M. A. Olson, A. Wallqvist, 2012, Journal of chemical theory and computation.

Identification of cooperative folding units in a set of native proteins

D. Covell, A. Wallqvist, G. Smythers, 1997, Protein science : a publication of the Protein Society.

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

Anders Wallqvist, Sheraz Gul, Melitta Schachner, 2014, Journal of neurochemistry.

Novel Burkholderia mallei Virulence Factors Linked to Specific Host-Pathogen Protein Interactions

J. Reifman, S. Rajagopala, Vesna Memisevic, 2013, Molecular & Cellular Proteomics.

Behavior of the hydrated electron at different temperatures: structure and absorption spectrum

B. Berne, A. Wallqvist, G. Martyna, 1988 .

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

J. Reifman, A. Wallqvist, T. Altes, 2020, Respiratory Physiology & Neurobiology.

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

J. Reifman, A. Wallqvist, V. Rakesh, 2018, Journal of biomechanical engineering.

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

Donald W. Lee, A. Wallqvist, S. Chaudhury, 2017, Front. Immunol..

Structure and dynamics of end-to-end loop formation of the penta-peptide Cys-Ala-Gly-Gln-Trp in implicit solvents.

A. Wallqvist, In-Chul Yeh, 2009, The journal of physical chemistry. B.

Localization of an excess electron in water clusters

B. Berne, D. Thirumalai, A. Wallqvist, 1986 .

Malaria Vaccine AMA1 Cross-Reactivity Induced by the Polyvalent Explains Enhanced Antibody Simulation of B Cell Affinity Maturation

J. Reifman, A. Wallqvist, S. Chaudhury, 2014 .

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

A. Wallqvist, D. Ippolito, M. AbdulHameed, 2016, Chemical research in toxicology.

Polarizable water at a hydrophobic wall

A. Wallqvist, 1990 .

A Web-Accessible Protein Structure Prediction Pipeline

Michael S. Lee, J. Reifman, N. Zavaljevski, 2009, 2009 DoD High Performance Computing Modernization Program Users Group Conference.

Path integral Monte Carlo study of the hydrated electron

Anders Wallqvist, Bruce J. Berne, B. Berne, 1987 .

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

J. Reifman, S. Rajagopala, Vesna Memisevic, 2017, PloS one.

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

D. Covell, E. Appella, A. Wallqvist, 1999, Journal of medicinal chemistry.

Azodicarbonamide inhibits HIV-1 replication by targeting the nucleocapsid protein

E. Sausville, D. Covell, A. Wallqvist, 1997, Nature Medicine.

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

A. Wallqvist, D. Ripoll, S. Teh, 2011, Antiviral research.

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

J. Reifman, A. Wallqvist, J. Feala, 2014, Journal of neuroscience research.

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

Kristopher D. Rawls, Venkat R. Pannala, Jamey D. Young, 2019, Toxicology and applied pharmacology.

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

J. Reifman, A. Wallqvist, Sridevi Nagaraja, 2014, The Journal of Immunology.

This information is current as of Chronic Wound Inflammation Causative Factors and Molecular Indicators Computational Approach To Characterize

J. Reifman, A. Wallqvist, Sridevi Nagaraja, 2014 .

DBSecSys: a database of Burkholderia mallei secretion systems

Li Cheng, Jaques Reifman, Nela Zavaljevski, 2014, BMC Bioinformatics.

Path-integral simulation of pure water☆

Anders Wallqvist, Bruce J. Berne, B. Berne, 1985 .

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

Chih-yuan Chiang, Vesna Memisevic, A. Wallqvist, 2015, Front. Microbiol..

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

A. Wallqvist, R. Printz, Patric Schyman, 2019, Front. Genet..

Age-dependent antibody profiles to plasmodium antigens are differentially associated with two artemisinin combination therapy outcomes in high transmission setting

A. Wallqvist, S. Chaudhury, B. Ogutu, 2022, Frontiers in Medicine.

On the origins of the hydrophobic effect: observations from simulations of n-dodecane in model solvents.

D. Covell, A. Wallqvist, Anders Wallqvist, 1996, Biophysical journal.

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

J. Reifman, A. Wallqvist, S. Laxminarayan, 2022, Journal of Computer-Aided Molecular Design.

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

A. Wallqvist, N. Waters, S. Chaudhury, 2016, Malaria Journal.

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

Leonard A. Smith, A. Wallqvist, D. Maloney, 2011, ACS medicinal chemistry letters.

Evaluation of selected chemotypes in coupled cellular and molecular target-based screens identifies novel HIV-1 zinc finger inhibitors.

D. Covell, D. Zaharevitz, A. Wallqvist, 1996, Journal of medicinal chemistry.

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

Ruili Huang, Anders Wallqvist, D. Covell, 2005, Biochemical pharmacology.

Differential Gene Expression as a Potential Classifier of 2-(4-Amino-3-methylphenyl)-5-fluorobenzothiazole-Sensitive and -Insensitive Cell Lines

E. Sausville, D. Covell, A. Monks, 2006, Molecular Pharmacology.

Differential Gene Expression as a potential classifier of 5F-203 Sensitive and Insensitive Cell Lines

E. Sausville, D. Covell, A. Monks, 2005 .

Intermolecular potentials for the water-benzene and the benzene-benzene systems calculated in an ab initio SCFCI approximation

Anders Wallqvist, Per Linse, G. Karlstroem, 1983 .

Intermolecular potentials for the water-benzene and the benzene-benzene systems calculated in an ab initio SCFCI approximation

G. Karlstroem, A. Wallqvist, P. Linse, 1983 .

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

Ruili Huang, Narmada Thanki, Anders Wallqvist, 2005, Proteins.

Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases

Ronald M. Levy, Anders Wallqvist, Yoshifumi Fukunishi, 2000, Bioinform..

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

Jaques Reifman, Anders Wallqvist, Francisco G. Vital-Lopez, 2013, BMC Systems Biology.

Properties of urea–water solvation calculated from a new ab initio polarizable intermolecular potential

P. Åstrand, A. Wallqvist, G. Karlström, 1991 .

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

Jaques Reifman, Xiaohui Jiang, Anders Wallqvist, 2008, BMC Bioinformatics.

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

Jaques Reifman, Francisco G. Vital-Lopez, Anders Wallqvist, 2015, PLoS Comput. Biol..

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

Leonard A. Smith, A. Wallqvist, G. Tawa, 2012, ACS medicinal chemistry letters.

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

P. Stewart, A. Wallqvist, G. James, 2019, Journal of bacteriology.

Inferring high-confidence human protein-protein interactions

J. Reifman, A. Wallqvist, Xueping Yu, 2012, BMC Bioinformatics.

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

Jennifer L. Dankmeyer, J. Reifman, N. Zavaljevski, 2016, Front. Cell. Infect. Microbiol..

Mining Host-Pathogen Protein Interactions to Characterize Burkholderia mallei Infectivity Mechanisms

Jaques Reifman, Nela Zavaljevski, Anders Wallqvist, 2015, PLoS Comput. Biol..

Rapid Countermeasure Discovery against Francisella tularensis Based on a Metabolic Network Reconstruction

Simon Daefler, Ali Navid, Anders Wallqvist, 2013, PloS one.

Incorporating intramolecular degrees of freedom in simulations of polarizable liquid water

A. Wallqvist, 1990 .

Molecular Models of Water: Derivation and Description

A. Wallqvist, R. Mountain, 2007 .

LIQUID DENSITIES AND STRUCTURAL PROPERTIES OF MOLECULAR MODELS OF WATER

P. Åstrand, A. Wallqvist, 1995 .

On the Implementation of Friedman Boundary Conditions in Liquid Water Simulations

A. Wallqvist, 1993 .

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

Anthony K. Felts, R. Levy, A. K. Felts, 2002, Proteins.

Metabolic responses in blood-stage malaria parasites associated with increased and decreased sensitivity to PfATP4 inhibitors

J. Reifman, A. Vaidya, A. Wallqvist, 2023, Malaria Journal.

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

J. Reifman, A. Vaidya, A. Wallqvist, 2022, Scientific Reports.

Pharmacogenomics of the National Cancer Institute’s 60-Tumor Cell Panel

Ruili Huang, David G. Covell, Anders Wallqvist, 2008 .

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

Ruili Huang, Anders Wallqvist, D. Covell, 2006, Genomics.

Path-integral Monte Carlo simulations of electron localization in water clusters

B. Berne, D. Thirumalai, A. Wallqvist, 1986 .

Atomic-scale analysis of the solvation thermodynamics of hydrophobic hydration.

S. Durell, A. Wallqvist, 1996, Biophysical journal.

Immunoprofiling Correlates of Protection Against SHIV Infection in Adjuvanted HIV-1 Pox-Protein Vaccinated Rhesus Macaques

A. Wallqvist, S. Chaudhury, M. Ackerman, 2021, Frontiers in Immunology.

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

Anders Wallqvist, Narender Singh, Mohamed Diwan M. AbdulHameed, 2012, Journal of Cheminformatics.

Molecular Dynamics Simulations of 2 m Aqueous Urea Solutions

G. Karlstroem, A. Wallqvist, P. Aåstrand, 1994 .

NONEMPIRICAL INTERMOLECULAR POTENTIALS FOR UREA-WATER SYSTEMS

P. Åstrand, A. Wallqvist, G. Karlström, 1994 .

Structural investigation of C4b‐binding protein by molecular modeling: Localization of putative binding sites

D. Covell, A. Wallqvist, B. Dahlbäck, 1998, Proteins.

Genome-scale model-based identification of metabolite indicators for early detection of kidney toxicity.

Venkat R. Pannala, Jamey D. Young, J. Reifman, 2019, Toxicological sciences : an official journal of the Society of Toxicology.

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

A. Wallqvist, S. Chaudhury, M. AbdulHameed, 2014, Bioorganic & medicinal chemistry.

Computer Simulation of Hydrophobic Hydration Forces on Stacked Plates at Short Range

Anders Wallqvist, Bruce J. Berne, B. Berne, 1995 .

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

A. Wallqvist, D. Ripoll, S. Chaudhury, 2017, Human vaccines & immunotherapeutics.

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

Jason A. Papin, Kristopher D. Rawls, Glynis L. Kolling, 2017, Nature Communications.

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

Anders Wallqvist, Alfred A. Rabow, Robert H. Shoemaker, 2003, Bioinform..

Development and validation of a mathematical model to simulate human cardiovascular and respiratory responses to battlefield trauma

J. Reifman, A. Wallqvist, S. Laxminarayan, 2022, International journal for numerical methods in biomedical engineering.

A strategy for evaluating pathway analysis methods

J. Reifman, A. Wallqvist, Xueping Yu, 2017, BMC Bioinformatics.

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

J. Reifman, A. Wallqvist, S. Prigge, 2020, Malaria Journal.

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

A. Wallqvist, G. Palacios, D. Ripoll, 2017, Human Vaccines & Immunotherapeutics.

Search for a Shared Genetic or Biochemical Basis for Biofilm Tolerance to Antibiotics across Bacterial Species

B. Mumey, A. Wallqvist, G. James, 2022, Antimicrobial agents and chemotherapy.

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

A. Wallqvist, D. Ripoll, S. Chaudhury, 2021, PLoS Comput. Biol..

Simulation of B Cell Affinity Maturation Explains Enhanced Antibody Cross-Reactivity Induced by the Polyvalent Malaria Vaccine AMA1

J. Reifman, A. Wallqvist, S. Chaudhury, 2014, The Journal of Immunology.

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

Jaques Reifman, Anders Wallqvist, Bora Sul, 2014, Comput. Biol. Medicine.

Genomics and metabolomics of early-stage thioacetamide-induced liver injury: An interspecies study between guinea pig and rat.

Venkat R. Pannala, A. Wallqvist, R. Printz, 2021, Toxicology and applied pharmacology.

TOXPANEL: A Gene-Set Analysis Tool to Assess Liver and Kidney Injuries

A. Wallqvist, Patric Schyman, V. Desai, 2021, Frontiers in Pharmacology.

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

Anders Wallqvist, Patric Schyman, Kelli L. Boyd, 2018, Front. Pharmacol..

PathNet: a tool for pathway analysis using topological information

Jaques Reifman, Anders Wallqvist, Bhaskar Dutta, 2012, Source Code for Biology and Medicine.

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

Anders Wallqvist, Rajkumar Bondugula, Michael S. Lee, 2008, Nucleic acids research.

Probing the Extent of Randomness in Protein Interaction Networks

Jaques Reifman, Anders Wallqvist, Joseph Ivanic, 2008, PLoS Comput. Biol..

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

Ruili Huang, Anders Wallqvist, D. Covell, 2007, Molecular Cancer Therapeutics.

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.

Ruili Huang, Anders Wallqvist, D. Covell, 2006, Journal of medicinal chemistry.

Bioinformatic Analysis of Patient-Derived ASPS Gene Expressions and ASPL-TFE3 Fusion Transcript Levels Identify Potential Therapeutic Targets

D. Covell, A. Wallqvist, S. Kenney, 2012, PloS one.

Free energy difference in indolicidin attraction to eukaryotic and prokaryotic model cell membranes.

Anders Wallqvist, A. Wallqvist, D. Ripoll, 2012, The journal of physical chemistry. B.

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

A. Wallqvist, In-Chul Yeh, 2011, The Journal of chemical physics.

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

Jaques Reifman, Chenggang Yu, Nela Zavaljevski, 2015, BMC Genomics.

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

Ruifeng Liu, Anders Wallqvist, Xueping Yu, 2015, Journal of Cheminformatics.

Identifying functional metabolic shifts in heart failure with the integration of omics data and a heart-specific, genome-scale model.

Kristopher D. Rawls, Bonnie V. Dougherty, A. Wallqvist, 2021, Cell reports.

Neuroprotective mechanisms activated in non-seizing rats exposed to sarin

A. Wallqvist, J. Dillman, Jerez A. Te, 2015, Brain Research.

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

J. Reifman, A. Wallqvist, S. Prigge, 2021, Malaria journal.

Metabolic host responses to malarial infection during the intraerythrocytic developmental cycle

Jaques Reifman, Xin Fang, Ping Ye, 2016, BMC Systems Biology.

A Novel Scoring Approach for Protein Co-Purification Data Reveals High Interaction Specificity

Jaques Reifman, Anders Wallqvist, Joseph Ivanic, 2009, PLoS Comput. Biol..

Screening the molecular surface of human anticoagulant protein C: A search for interaction sites

Bruno O. Villoutreix, David G. Covell, Anna M. Blom, 2001, J. Comput. Aided Mol. Des..

Modeling Phenotypic Metabolic Adaptations of Mycobacterium tuberculosis H37Rv under Hypoxia

Jaques Reifman, Xin Fang, Anders Wallqvist, 2012, PLoS Comput. Biol..

Mining kidney toxicogenomic data by using gene co-expression modules

Anders Wallqvist, Mohamed Diwan M. AbdulHameed, Jonathan D. Stallings, 2016, BMC Genomics.

Exploring Polypharmacology Using a ROCS-Based Target Fishing Approach

Anders Wallqvist, Narender Singh, Mohamed Diwan M. AbdulHameed, 2012, J. Chem. Inf. Model..

Assessing Deep and Shallow Learning Methods for Quantitative Prediction of Acute Chemical Toxicity

Ruifeng Liu, Anders Wallqvist, Kyle P Glover, 2018, Toxicological sciences : an official journal of the Society of Toxicology.

Fold Recognition using the OPLS All-Atom Potential and the Surface Generalized Born Solvent Model

Anthony K. Felts, R. Levy, A. K. Felts, 2002 .

Cooperative folding units of escherichia coli tryptophan repressor.

D. Covell, A. Wallqvist, J. Carey, 1999, Biophysical journal.

Predicting changes in renal metabolism after compound exposure with a genome-scale metabolic model.

Kristopher D. Rawls, Venkat R. Pannala, Bonnie V. Dougherty, 2020, Toxicology and applied pharmacology.

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

A. Wallqvist, R. Printz, M. Shiota, 2018, Toxicology in vitro : an international journal published in association with BIBRA.

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

Ruifeng Liu, Anders Wallqvist, Xueping Yu, 2016, Chemical research in toxicology.

QSAR Classification Model for Antibacterial Compounds and Its Use in Virtual Screening

Ruifeng Liu, Anders Wallqvist, Narender Singh, 2012, J. Chem. Inf. Model..

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

A. Wallqvist, D. Ippolito, W. Dennis, 2018, Toxicologic pathology.

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

J. Reifman, A. Wallqvist, S. Prigge, 2021, Antimicrobial Agents and Chemotherapy.

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

Anders Wallqvist, Mohamed Diwan M. AbdulHameed, A. Wallqvist, 2016, Journal of applied toxicology : JAT.

Molecular Dynamics Study of the Dependence of Water Solvation Free Energy on Solute Curvature and Surface Area

B. Berne, A. Wallqvist, 1995 .

vNN Web Server for ADMET Predictions

Ruifeng Liu, Valmik Desai, Anders Wallqvist, 2017, Front. Pharmacol..

2D SMARTCyp Reactivity-Based Site of Metabolism Prediction for Major Drug-Metabolizing Cytochrome P450 Enzymes

Jin Liu, Ruifeng Liu, Anders Wallqvist, 2012, J. Chem. Inf. Model..

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

Jaques Reifman, Xin Hu, Anders Wallqvist, 2008, Chemistry Central journal.

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

J. Reifman, A. Wallqvist, S. Prigge, 2019, Malaria journal.

In silico analyses of substrate interactions with human serum paraoxonase 1

Anders Wallqvist, A. Wallqvist, Xin Hu, 2009, Proteins.

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

D. Covell, A. Wallqvist, A. Blom, 1998, Biochimica et biophysica acta.

Assessing Kidney Injury Induced by Mercuric Chloride in Guinea Pigs with In Vivo and In Vitro Experiments

Venkat R. Pannala, A. Wallqvist, R. Printz, 2023, International journal of molecular sciences.

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

D. Covell, A. Wallqvist, D G Covell, 1997, Journal of molecular biology.

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

Ajit Jadhav, Anders Wallqvist, Dagmar H. Leary, 2013, Journal of medicinal chemistry.

Quantitative Predictions of Binding Free Energy Changes in Drug-Resistant Influenza Neuraminidase

Jaques Reifman, Jin Liu, Anders Wallqvist, 2012, PLoS Comput. Biol..

Characterization of Chemically Induced Liver Injuries Using Gene Co-Expression Modules

Anders Wallqvist, Mohamed Diwan M. AbdulHameed, Gregory J. Tawa, 2014, PloS one.

Merging Applicability Domains for in Silico Assessment of Chemical Mutagenicity

Ruifeng Liu, Anders Wallqvist, A. Wallqvist, 2014, J. Chem. Inf. Model..

A reaction path study of the catalysis and inhibition of the Bacillus anthracis CapD γ-glutamyl transpeptidase.

Anders Wallqvist, A. Wallqvist, A. Friedlander, 2014, Biochemistry.

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

Anders Wallqvist, A. Wallqvist, I. Khavrutskii, 2011, Journal of chemical theory and computation.

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

A. Wallqvist, Patric Schyman, Ruifeng Liu, 2016, ACS omega.

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

Ruifeng Liu, Anders Wallqvist, Patric Schyman, 2016, J. Chem. Inf. Model..

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

Ruifeng Liu, Anders Wallqvist, Patric Schyman, 2015, J. Chem. Inf. Model..

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

Ruifeng Liu, Anders Wallqvist, Gregory Tawa, 2012, Chemical research in toxicology.

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

R. Levy, A. Wallqvist, and Emilio Gallicchio, 2001 .

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

Valmik Desai, Anders Wallqvist, Daniel R. Ripoll, 2017, PLoS neglected tropical diseases.

Tegaserod mimics the neurostimulatory glycan polysialic acid and promotes nervous system repair

A. Wallqvist, A. Wallqvist, D. Ripoll, 2013, Neuropharmacology.

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

Jaques Reifman, Nela Zavaljevski, Anders Wallqvist, 2016, BMC Bioinformatics.

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

Michael S. Lee, A. Wallqvist, Xin Hu, 2009, Biochemistry.

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

Arne Elofsson, Anders Wallqvist, Berk Hess, 2019, PLoS Comput. Biol..

New intermolecular energy calculation scheme: applications to potential surface and liquid properties of water

G. Karlstroem, A. Wallqvist, P. Ahlstroem, 1990 .

Effective potentials for liquid water using polarizable and nonpolarizable models

Anders Wallqvist, Bruce J. Berne, B. Berne, 1993 .

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

A. Wallqvist, I. Khavrutskii, 2017 .

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

A. Wallqvist, N. Waters, S. Chaudhury, 2017, Scientific Reports.

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

Kristopher D. Rawls, Matthew L. Jenior, Bonnie V. Dougherty, 2021 .

Exploiting Physical Parallelism Using Supercomputers: Two Examples from Chemical Physics

Anders Wallqvist, Bruce J. Berne, Chani Pangali, 1987, Computer.

Properties of flexible water models

A. Wallqvist, O. Teleman, 1991 .

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

Venkat R. Pannala, Jamey D. Young, J. Reifman, 2019, Front. Physiol..

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

Jaques Reifman, Xin Fang, Anders Wallqvist, 2010, BMC Systems Biology.

Mining kidney toxicogenomic data by using gene co-expression modules

Jonathan D. Stallings, A. Wallqvist, D. Ippolito, 2016, BMC Genomics.

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

J. Reifman, A. Vaidya, A. Wallqvist, 2022, Scientific Reports.

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

A. Wallqvist, S. Prigge, Shivendra G. Tewari, 2020, PLoS pathogens.

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

J. Reifman, A. Wallqvist, S. Prigge, 2020, Malaria Journal.

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

Jaques Reifman, Anders Wallqvist, Xin Fang, 2014, Molecular bioSystems.

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

A. Wallqvist, R. Printz, Patric Schyman, 2020, International journal of molecular sciences.

Ewald summation retards translational motion in molecular dynamics simulation of water

A. Wallqvist, O. Teleman, 1990 .

Evidence of probabilistic behaviour in protein interaction networks

Jaques Reifman, Anders Wallqvist, Joseph Ivanic, 2008, BMC Systems Biology.

HYDROPHOBIC INTERACTION BETWEEN A METHANE MOLECULE AND A PARAFFIN WALL IN LIQUID WATER

B. Berne, A. Wallqvist, 1988 .

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

Ruili Huang, Anders Wallqvist, D. Covell, 2006, Molecular Cancer Therapeutics.

Metabolic changes accompanying the loss of fumarate hydratase and malate–quinone oxidoreductase in the asexual blood stage of Plasmodium falciparum

A. Wallqvist, S. Prigge, Shivendra G. Tewari, 2022, The Journal of biological chemistry.

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

A. Wallqvist, M. Schachner, S. Chaudhury, 2016, Journal of neurochemistry.

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

A. Wallqvist, D. Ripoll, S. Chaudhury, 2016, Biophysical journal.

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

A. Wallqvist, D. Ripoll, S. Chaudhury, 2019, Front. Cell. Infect. Microbiol..

Identifying Cytochrome P450 Functional Networks and Their Allosteric Regulatory Elements

Jin Liu, A. Wallqvist, G. Tawa, 2013, PloS one.

A stochastic B cell affinity maturation model to characterize mechanisms of protection for tetravalent dengue vaccine constructs

A. Wallqvist, Hung D. Nguyen, V. Pannala, 2023, Frontiers in molecular biosciences.

Stochastic Model of the Adaptive Immune Response Predicts Disease Severity and Captures Enhanced Cross-Reactivity in Natural Dengue Infections

A. Wallqvist, S. Chaudhury, A. Waickman, 2021, Frontiers in Immunology.

Intermolecular potential variation due to intramolecular rotation in molecules

A. Wallqvist, 1991 .

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

Alexey V Zakharov, Ruifeng Liu, Anders Wallqvist, 2012, Future medicinal chemistry.

Modeling synergistic drug inhibition of Mycobacterium tuberculosis growth in murine macrophages.

Jaques Reifman, Anders Wallqvist, Xin Fang, 2011, Molecular bioSystems.

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

Jaques Reifman, Ruifeng Liu, Anders Wallqvist, 2014, BMC Bioinformatics.

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

Jamey D. Young, J. Reifman, A. Wallqvist, 2018, Scientific Reports.

Molecular dynamics study of a hydrophobic aggregate in an aqueous solution of methane

Anders Wallqvist, A. Wallqvist, 1991 .

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

Jaques Reifman, Xin Fang, Anders Wallqvist, 2009, BMC Systems Biology.

Intermolecular Interactions of Urea and Water

P. Åstrand, A. Wallqvist, G. Karlström, 1991 .

Accelerating Biomedical Research in Designing Diagnostic Assays, Drugs, and Vaccines

Jaques Reifman, Rajkumar Bondugula, Xin Hu, 2010, Computing in Science & Engineering.

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

Jason A. Papin, Kristopher D. Rawls, Bonnie V. Dougherty, 2019, Comput. Biol. Medicine.

Can computationally designed protein sequences improve secondary structure prediction?

Rajkumar Bondugula, Anders Wallqvist, Michael S. Lee, 2011, Protein engineering, design & selection : PEDS.

Ruifeng Liu, Anders Wallqvist, A. Wallqvist, 2018, J. Chem. Inf. Model..

Evidence of interaction between humoral immunity and drug half-life in determining treatment outcome for artemisinin combination therapy in high transmission settings in western Kenya

A. Wallqvist, S. Chaudhury, B. Ogutu, 2020 .

Molecular Classification of Cancer : Unsupervised Self-Organizing Map Analysis of Gene Expression Microarray Data 1

D. Covell, A. Wallqvist, A. Rabow, 2003 .

Exploring chemical reaction mechanisms through harmonic Fourier beads path optimization.

A. Wallqvist, I. Khavrutskii, Jason B. Smith, 2013, The Journal of chemical physics.

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

Ruifeng Liu, Anders Wallqvist, Kyle P Glover, 2018, J. Chem. Inf. Model..

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

Ruifeng Liu, Anders Wallqvist, Mohamed Diwan M. AbdulHameed, 2017, J. Chem. Inf. Model..

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

A. Wallqvist, D. Ripoll, S. Chaudhury, 2015, Biochemistry and biophysics reports.

Evidence of probabilistic behaviour in protein interaction networks

J. Reifman, A. Wallqvist, J. Ivanic, 2008, BMC Systems Biology.

A strategy for evaluating pathway analysis methods

Jaques Reifman, Chenggang Yu, Anders Wallqvist, 2017, BMC Bioinformatics.

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

J. Reifman, A. Wallqvist, Sridevi Nagaraja, 2014, Journal of Immunology.

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

J. Reifman, A. Wallqvist, Sridevi Nagaraja, 2014, Journal of Immunology.

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

Ruifeng Liu, Anders Wallqvist, Hao Wang, 2018, J. Chem. Inf. Model..

Using a Graph Convolutional Neural Network Model to Identify Bile Salt Export Pump Inhibitors

A. Wallqvist, M. AbdulHameed, Ruifeng Liu, 2023, ACS omega.

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

A. Wallqvist, D. Ippolito, W. Dennis, 2018, Toxicologic pathology.

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

A. Wallqvist, 1991 .

Modeling synergistic drug inhibition of Mycobacterium tuberculosis growth in murine macrophages.

J. Reifman, A. Wallqvist, X. Fang, 2011, Molecular bioSystems.

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

J. Reifman, A. Wallqvist, X. Fang, 2009, BMC Systems Biology.

A Systems Biology Framework for Modeling Metabolic Enzyme Inhibition of Mycobacterium Tuberculosis

J. Reifman, A. Wallqvist, Xin Fang, 2009 .

Host Response to Environmental Hazards: Using Literature, Bioinformatics, and Computation to Derive Candidate Biomarkers of Toxic Industrial Chemical Exposure

Jaques Reifman, Anders Wallqvist, Jonathan D. Stallings, 2015 .

Simulation of B Cell Affinity Maturation Explains Enhanced Antibody Cross-Reactivity Induced by the Polyvalent Malaria Vaccine AMA1

J. Reifman, A. Wallqvist, Sidhartha Chaudhury, 2014, The Journal of Immunology.

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

A. Wallqvist, M. Feasel, Ruifeng Liu, 2018, Journal of Chemical Information and Modeling.

A. Wallqvist, Ruifeng Liu, 2018, Journal of chemical information and modeling.

Pressure dependence of methane solvation in aqueous mixtures and the relation to the structure of liquid water

A. Wallqvist, 1992 .

Spontaneous buckling of lipid bilayer and vesicle budding induced by antimicrobial peptide magainin 2: a coarse-grained simulation study.

A. Wallqvist, H. Woo, 2011, The journal of physical chemistry. B.

Inferring high-confidence human protein-protein interactions

Jaques Reifman, Anders Wallqvist, Xueping Yu, 2012, BMC Bioinformatics.

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

A. Wallqvist, M. AbdulHameed, F. Sharom, 2014, Bioorganic & medicinal chemistry.

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

Anders Wallqvist, Mark A Olson, Michael S. Lee, 2008, Biophysical journal.

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

J. Reifman, A. Wallqvist, X. Fang, 2014, Molecular bioSystems.

On the stability of type I gas hydrates in the presence of methanol

A. Wallqvist, 1992 .

ToxProfiler: Toxicity-target profiler based on chemical similarity

Valmik Desai, Anders Wallqvist, Mohamed Diwan M. AbdulHameed, 2021, Computational Toxicology.

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

Anders Wallqvist, Ilja V. Khavrutskii, Donald W. Lee, 2017, Front. Immunol..

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

J. Reifman, A. Wallqvist, Sridevi Nagaraja, 2014, Journal of Immunology.