Wallqvist, Anders: search on Z-Library

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1

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

Liu, Ruifeng, AbdulHameed, Mohamed Diwan M., Wallqvist, Anders

Journal:

Frontiers in Chemistry

Year:

2019

Language:

english

File:

PDF, 550 KB

english, 2019

2

Comment on: ‘‘Water–water and water–ion potential functions including terms for many-body effects,’’ T. P. Lybrand and P. Kollman, J. Chem. Phys. 83, 2923 (1985), and on ‘‘Calculation of free energy changes in ion–water clusters using nonadditive potentials and the Monte Carlo method,’’ P. Cieplak, T. P. Lybrand, and P. Kollman, J. Chem. Phys. 86, 6393 (1987)

Berne, Bruce J., Wallqvist, Anders

Journal:

The Journal of Chemical Physics

Year:

1988

Language:

english

File:

PDF, 372 KB

english, 1988

3

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

Pannala, Venkat R., Estes, Shanea K., Rahim, Mohsin, Trenary, Irina, OâBrien, Tracy P., Shiota, Chiyo, Printz, Richard L., Reifman, Jaques, Shiota, Masakazu, Young, Jamey D., Wallqvist, Anders

Journal:

International Journal of Molecular Sciences

Year:

2020

File:

PDF, 3.20 MB

2020

4

Investigation of the temperature dependence of dielectric relaxation in liquid water by THz reflection spectroscopy and molecular dynamics simulation

Ro̸nne, Cecilie, Thrane, Lars, Åstrand, Per-Olof, Wallqvist, Anders, Mikkelsen, Kurt V., Keiding, So̸ren R.

Journal:

The Journal of Chemical Physics

Year:

1997

Language:

english

File:

PDF, 560 KB

english, 1997

5

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

Xiaohui Jiang, Kamal Kumar, Xin Hu, Anders Wallqvist, Jaques Reifman

Journal:

Chemistry Central Journal

Year:

2008

Language:

english

File:

PDF, 407 KB

english, 2008

6

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

Tewari, Shivendra G., Rajaram, Krithika, Schyman, Patric, Swift, Russell, Reifman, Jaques, Prigge, Sean T., Wallqvist, Anders

Journal:

Malaria Journal

Year:

2019

Language:

english

File:

PDF, 7.14 MB

english, 2019

7

[IEEE 2009 DoD High Performance Computing Modernization Program Users Group Conference (HPCMP-UGC) - San Diego, CA, USA (2009.06.15-2009.06.18)] 2009 DoD High Performance Computing Modernization Program Users Group Conference - A Web-Accessible Protein Structure Prediction Pipeline

Lee, Michael S., Bondugula, Rajkumar, Desai, Valmik, Zavaljevski, Nela, Yeh, In-Chul, Wallqvist, Anders, Reifman, Jaques

Year:

2009

Language:

english

File:

PDF, 589 KB

english, 2009

8

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

Liu, Ruifeng, Wallqvist, Anders

Journal:

Journal of Chemical Information and Modeling

Year:

2018

Language:

english

File:

PDF, 1.08 MB

english, 2018

9

In silico co-factor balance estimation using constraint-based modelling informs metabolic engineering in Escherichia coli

de Arroyo Garcia, Laura, Jones, Patrik R., Wallqvist, Anders

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 9.88 MB

2020

10

In silico analyses of substrate interactions with human serum paraoxonase 1

Xin Hu, Xiaohui Jiang, David E. Lenz, Douglas M. Cerasoli, Anders Wallqvist

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2009

Language:

english

File:

PDF, 607 KB

english, 2009

11

Azodicarbonamide inhibits HIV-1 replication by targeting the nucleocapsid protein

Clanton, David, Buckheit, Robert W., Covell, David G., Wallqvist, Anders, McDonnell, Nazli B., DeGuzman, Roberto N., Summers, Michael F., Rice, William G., Turpin, Jim A., Huang, Mingjun

Journal:

Nature Medicine

Year:

1997

File:

PDF, 525 KB

1997

12

A systems biology framework for modeling metabolic enzyme inhibition ofMycobacterium tuberculosis

Xin Fang, Anders Wallqvist, Jaques Reifman

Journal:

BMC Systems Biology

Year:

2009

Language:

english

File:

PDF, 1.81 MB

english, 2009

13

Free-Energy Profiles of Membrane Insertion of the M2 Transmembrane Peptide from Influenza A Virus

Yeh, In-Chul, Olson, Mark A., Lee, Michael S., Wallqvist, Anders

Journal:

Biophysical Journal

Year:

2008

Language:

english

File:

PDF, 393 KB

english, 2008

14

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

Vital-Lopez, Francisco G, Wallqvist, Anders, Reifman, Jaques

Journal:

BMC Systems Biology

Year:

2013

Language:

english

File:

PDF, 443 KB

english, 2013

15

On the basis set superposition error in the evaluation of water dimer interactions

Aastrand, Per Olof, Wallqvist, Anders, Karlstroem, Gunnar

Journal:

Journal of Physical Chemistry

Year:

1991

Language:

english

File:

PDF, 260 KB

english, 1991

16

Properties of flexible water models

Wallqvist, Anders, Teleman, Olle

Journal:

Molecular Physics

Year:

1991

Language:

english

File:

PDF, 955 KB

english, 1991

17

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

Yu, Chenggang, Boutté, Angela, Yu, Xueping, Dutta, Bhaskar, Feala, Jacob D., Schmid, Kara, Dave, Jitendra, Tawa, Gregory J., Wallqvist, Anders, Reifman, Jaques

Journal:

Journal of Neuroscience Research

Year:

2015

Language:

english

File:

PDF, 1.05 MB

english, 2015

18

A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types

Seif, Yara, Monk, Jonathan M., Mih, Nathan, Tsunemoto, Hannah, Poudel, Saugat, Zuniga, Cristal, Broddrick, Jared, Zengler, Karsten, Palsson, Bernhard O., Wallqvist, Anders

Journal:

PLoS Computational Biology

Year:

2019

File:

PDF, 3.21 MB

2019

19

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

AbdulHameed, Mohamed Diwan M., Pannala, Venkat R., Wallqvist, Anders

Journal:

Frontiers in Genetics

Year:

2019

Language:

english

File:

PDF, 2.00 MB

english, 2019

20

A systematic evaluation of Mycobacterium tuberculosis Genome-Scale Metabolic Networks

LÃ³pez-Agudelo, VÃctor A., Mendum, Tom A., Laing, Emma, Wu, HuiHai, Baena, Andres, Barrera, Luis F., Beste, Dany J. V., Rios-Estepa, Rigoberto, Wallqvist, Anders

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 4.52 MB

2020

21

A toxicogenomic approach to assess kidney injury induced by mercuric chloride in rats

Schyman, Patric, Printz, Richard L., AbdulHameed, Mohamed Diwan M., Estes, Shanea K., Shiota, Chiyo, Shiota, Masakazu, Wallqvist, Anders

Journal:

Year:

2020

File:

PDF, 3.11 MB

2020

22

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, Emilio Gallicchio, Anders Wallqvist, Ronald M. Levy

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2002

Language:

english

File:

PDF, 327 KB

english, 2002

23

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

Liu, Ruifeng, Liu, Jin, Tawa, Greg, Wallqvist, Anders

Journal:

Journal of Chemical Information and Modeling

Year:

2012

Language:

english

File:

PDF, 3.15 MB

english, 2012

24

[IEEE 2008 DoD HPCMP Users Group Conference - Seattle, WA, USA (2008.07.14-2008.07.17)] 2008 DoD HPCMP Users Group Conference - Membrane Insertion Profiles of Peptides Probed by Molecular Dynamics Simulations

Yeh, In-Chul, Olson, Mark A., Lee, Michael S., Wallqvist, Anders

Year:

2008

Language:

english

File:

PDF, 695 KB

english, 2008

25

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

AbdulHameed, Mohamed Diwan M., Tawa, Gregory J., Kumar, Kamal, Ippolito, Danielle L., Lewis, John A., Stallings, Jonathan D., Wallqvist, Anders, Chan, Christina

Journal:

Year:

2014

Language:

english

File:

PDF, 2.42 MB

english, 2014

26

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

Schyman, Patric, Printz, Richard L., Estes, Shanea K., Boyd, Kelli L., Shiota, Masakazu, Wallqvist, Anders

Journal:

Frontiers in Pharmacology

Year:

2018

Language:

english

File:

PDF, 6.09 MB

english, 2018

27

Classification of scaffold-hopping approaches

Hongmao Sun, Gregory Tawa, Anders Wallqvist

Journal:

Drug Discovery Today

Year:

2012

Language:

english

File:

PDF, 1.66 MB

english, 2012

28

Synthesis and Biological Properties of Novel Pyridinioalkanoyl Thiolesters (PATE) as Anti-HIV-1 Agents That Target the Viral Nucleocapsid Protein Zinc Fingers

Turpin, Jim A., Song, Yongsheng, Inman, John K., Huang, Mingjun, Wallqvist, Anders, Maynard, Andrew, Covell, David G., Rice, William G., Appella, Ettore

Journal:

Journal of Medicinal Chemistry

Year:

1999

Language:

english

File:

PDF, 302 KB

english, 1999

29

Identifying Cytochrome P450 Functional Networks and Their Allosteric Regulatory Elements

Liu, Jin, Tawa, Gregory J., Wallqvist, Anders, Parker, Emily

Journal:

Year:

2013

Language:

english

File:

PDF, 1.52 MB

english, 2013

30

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

Liu, Ruifeng, Yu, Xueping, Wallqvist, Anders

Journal:

Journal of Cheminformatics

Year:

2015

Language:

english

File:

PDF, 422 KB

english, 2015

31

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

David G. Covell, Anders Wallqvist, Ruili Huang, Narmada Thanki, Alfred A. Rabow, Xiang-Jun Lu

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 822 KB

english, 2005

32

Ewald summation retards translational motion in molecular dynamics simulation of water

Olle Teleman, Anders Wallqvist

Journal:

International Journal of Quantum Chemistry

Year:

1990

Language:

english

File:

PDF, 240 KB

english, 1990

33

Ewald summation retards translational motion in molecular dynamics simulation of water

Olle Teleman, Anders Wallqvist

Journal:

International Journal of Quantum Chemistry

Year:

1992

Language:

english

File:

PDF, 85 KB

english, 1992

34

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

Wallqvist, Anders, Gallicchio, Emilio, Levy, Ronald M.

Journal:

Journal of Physical Chemistry B

Year:

2001

Language:

english

File:

PDF, 175 KB

english, 2001

35

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

Te, Jerez A., AbdulHameed, Mohamed Diwan M., Wallqvist, Anders

Journal:

Journal of Applied Toxicology

Year:

2016

Language:

english

File:

PDF, 527 KB

english, 2016

36

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

Tewari, Shivendra G., Prigge, Sean T., Reifman, Jaques, Wallqvist, Anders

Journal:

International Journal for Parasitology Drugs and Drug Resistance

Year:

2017

Language:

english

File:

PDF, 1.32 MB

english, 2017

37

Maximum entropy and population heterogeneity in continuous cell cultures

Fernandez-de-Cossio-Diaz, Jorge, Mulet, Roberto, Wallqvist, Anders

Journal:

PLoS Computational Biology

Year:

2019

Language:

english

File:

PDF, 2.62 MB

english, 2019

38

Chemoinformatic Analysis of NCI Preclinical Tumor Data: Evaluating Compound Efficacy from Mouse Xenograft Data, NCI-60 Screening Data, and Compound Descriptors

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

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 523 KB

english, 2007

39

Evaluating Chemical Structure Similarity as an Indicator of Cellular Growth Inhibition

Wallqvist, Anders, Huang, Ruili, Thanki, Narmada, Covell, David G.

Journal:

Journal of Chemical Information and Modeling

Year:

2006

Language:

english

File:

PDF, 114 KB

english, 2006

40

Probing the Extent of Randomness in Protein Interaction Networks

Ivanic, Joseph, Wallqvist, Anders, Reifman, Jaques, Rost, Burkhard

Journal:

PLoS Computational Biology

Year:

2008

Language:

english

File:

PDF, 466 KB

english, 2008

41

Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli

Du, Bin, Yang, Laurence, Lloyd, Colton J., Fang, Xin, Palsson, Bernhard O., Wallqvist, Anders

Journal:

PLoS Computational Biology

Year:

2019

File:

PDF, 2.47 MB

2019

42

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

Swift, Russell P., Rajaram, Krithika, Liu, Hans B., Dziedzic, Amanda, Jedlicka, Anne E., Roberts, Aleah D., Matthews, Krista A., Jhun, Hugo, Bumpus, Namandje N., Tewari, Shivendra G., Wallqvist, Ander

Journal:

Year:

2020

File:

PDF, 5.49 MB

2020

43

Incorporating intramolecular degrees of freedom in simulations of polarizable liquid water

Anders Wallqvist

Journal:

Chemical Physics

Year:

1990

Language:

english

File:

PDF, 1014 KB

english, 1990

44

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

Anna M. Blom, David G. Covell, Anders Wallqvist, Björn Dahlbäck, Bruno O. Villoutreix

Journal:

Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology

Year:

1998

Language:

english

File:

PDF, 576 KB

english, 1998

45

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

Singh, Narender, Chaudhury, Sidhartha, Liu, Ruifeng, AbdulHameed, Mohamed Diwan M., Tawa, Gregory, Wallqvist, Anders

Journal:

Journal of Chemical Information and Modeling

Year:

2012

Language:

english

File:

PDF, 1.84 MB

english, 2012

46

Locally Weighted Learning Methods for Predicting Dose-Dependent Toxicity with Application to the Human Maximum Recommended Daily Dose

Liu, Ruifeng, Tawa, Gregory, Wallqvist, Anders

Journal:

Chemical Research in Toxicology

Year:

2012

Language:

english

File:

PDF, 2.43 MB

english, 2012

47

Nonequilibrium Phase Transitions Associated with DNA Replication

Woo, Hyung-June, Wallqvist, Anders

Journal:

Physical Review Letters

Year:

2011

Language:

english

File:

PDF, 311 KB

english, 2011

48

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

Yu, Xueping, Ivanic, Joseph, Wallqvist, Anders, Reifman, Jaques, Stormo, Gary D.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.72 MB

english, 2009

49

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

Schyman, Patric, Liu, Ruifeng, Wallqvist, Anders

Journal:

Journal of Chemical Information and Modeling

Year:

2016

Language:

english

File:

PDF, 2.13 MB

english, 2016

50

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

Ripoll, Daniel R., Khavrutskii, Ilja, Wallqvist, Anders, Chaudhury, Sidhartha

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 2.79 MB

english, 2016

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