Chemistry and Pharmaceutical Sciences

Research Output 1977 2020

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2019

A protocol for one-step differentiation of human induced pluripotent stem cells into mature podocytes

Murphy, C., Feifel, E., Jennings, P., Gstraunthaler, G. & Wilmes, A., 2019, Cell-Based Assays Using iPSCs for Drug Development and Testing. Mandenius, C. F. & Ross, J. (eds.). Humana Press Inc., p. 93-99 7 p. (Methods in Molecular Biology; vol. 1994).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Induced Pluripotent Stem Cells
Podocytes
Glomerular Filtration Barrier
Cell Culture Techniques
Epithelial Cells

Cation affinities throughout the periodic table

Boughlala, Z., Fonseca Guerra, C. & Bickelhaupt, F. M., 2019, Computational Chemistry. van Eldik, R. & Puchta, R. (eds.). Academic Press Inc., p. 123-158 36 p. (Advances in Inorganic Chemistry; vol. 73).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Cations
Lewis Bases
Alkali Metals
Molecular orbitals
Hydrides

Understanding the Governance of the Engaged and Entrepreneurial University: Towards a New Research and Policy Agenda

Blankesteijn, M. L., Sam, P. N. & van der Sijde, P. C., Oct 2019, Developing Engaged and Entrepreneurial Universities. Kliewe, T., C., K., C., P. & Baaken, T. (eds.). Springer, p. 43-53 11 p.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

governance
university
rent
twenty-first century
economy
2018

Analysis of metabolites from the tricarboxylic acid cycle for yeast and bacteria samples using gas chromatography mass spectrometry

Seifar, R. M., ten Pierick, A. & van Dam, P. T. N., 2018, Clinical Metabolomics: methods and protocols. Giera, M. (ed.). Humana Press Inc, p. 277-282 6 p. (Methods in Molecular Biology; vol. 1730).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Citric Acid Cycle
Gas Chromatography-Mass Spectrometry
Yeasts
Bacteria
Fumarates

A Structural Framework for GPCR Chemogenomics: What’s In a Residue Number?

Vass, M., Kooistra, A. J., Verhoeven, S., Gloriam, D., de Esch, I. J. P. & de Graaf, C., 2018, Computational Methods for GPCR Drug Discovery. Heifetz, A. (ed.). Humana Press Inc, p. 73-113 41 p. (Methods in Molecular Biology; vol. 1705).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

G-Protein-Coupled Receptors
Binding Sites
Ligands
Workflow
Mutation

Duurzame energietransitie door demonstratie

Bossink, B., Jan 2018, Adaptief Bestuur: Essays over adaptiviteit en openbaar bestuur. Mettau, P. & Hulsenboom, Z. (eds.). Den Haag: Ministerie van Binnenlandse Zaken en Koninkrijksrelaties, p. 100-113 14 p. (Publicaties; vol. 110379).

Research output: Chapter in Book / Report / Conference proceedingChapterProfessional

Open Access
2017

1.15 - Structural Chemogenomics Databases to Navigate Protein–Ligand Interaction Space

Kanev, G. K., Kooistra, A. J., de Esch, I. J. P. & de Graaf, C., 2017, 1.15 - Structural Chemogenomics Databases to Navigate Protein–Ligand Interaction Space. Comprehensive Medicinal Chemistry III ed. Elsvier, Vol. 1. p. 444-471

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Ligands
Proteins
Proteome
Bioactivity
Data mining

Chemokine receptor oligomerization to tweak chemotactic responses

Vischer, H. F., 2017, G-Protein-Coupled Receptor Dimers. p. 233-272 (The Receptors; vol. 33).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Chemokine Receptors
Cell Movement
G-Protein-Coupled Receptors
Chemokines
Pharmacology

Kinase-Centric Computational Drug Development

Kooistra, A. J. & Volkamer, A., 1 Jan 2017, Annual Reports in Medicinal Chemistry. Academic Press Inc., Vol. 50. p. 197-236 (Annual Reports in Medicinal Chemistry; vol. 50).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Phosphotransferases
Pharmaceutical Preparations
Bioactivity
Drug Design
Sequence Analysis

Ligand-binding kinetics on histamine receptors

Bosma, R., Mocking, T. A. M., Leurs, R. & Vischer, H. F., 2017, Histamine receptors as drug targets. Humana Press, p. 115-155 (Methods in pharmacology and toxicology).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Histamine Receptors
Ligands
Pharmaceutical Preparations
Histamine Antagonists

Methods to study the molecular pharmacology of the histamine H4 receptor

Verweij, E. W. E., Leurs, R. & Vischer, H. F., 2017, Histamine receptors as drug targets. Humana Press, p. 157-181 (Methods in pharmacology and toxicology).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Histamine Receptors
Pharmacology
Ligands
Animal Disease Models
Drug Discovery
2016

Capillary zone electrophoresis-mass spectrometry of intact proteins

Domínguez-Vega, E., Haselberg, R. & Somsen, G. W., 2016, Capillary Electrophoresis of Proteins and Peptides: Methods and Protocols. Tran, N. T. & Taverna, M. (eds.). Humana Press Inc, p. 25-41 17 p. (Methods in Molecular Biology; vol. 1466).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Capillary Electrophoresis
Mass Spectrometry
Proteins
Human Growth Hormone
Muramidase

GPU Acceleration for Density Functional Theory with Slater-Type Orbitals

van Schoot, H. & Visscher, L., 2016, Electronic Structure Calculations on Graphics Processing Units: From Quantum Chemistry to Condensed Matter Physics. Walker, R. C. & Gotz, A. W. (eds.). Wiley Blackwell, p. 101-113 13 p.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Density functional theory
Program processors
Coulomb interactions
Hardware
Atoms

Intact protein analysis by capillary electrophoresis - mass spectrometry.

Haselberg, R. & Somsen, G. W., 2016, Capillary electrophoresis - Mass Spectrometry: Principles and Applications.. De Jong, G. J. (ed.). Wiley, p. 159-192

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

In Vitro to In Vivo Relationships with Respect to Kidney Safety Biomarkers

Jennings, P., 1 Jan 2016, Drug Discovery Toxicology: From Target Assessment to Translational Biomarkers. Wiley, p. 458-461 4 p.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Biomarkers
Cell culture
Interleukins
Kidney
Safety

Molecular Aspects of Histamine Receptors

Mocking, T., Bosma, R., Rahman, S. N., Verweij, E. W. E., McNaught-Flores, D. A., Vischer, H. F. & Leurs, R., 2016, Histamine Receptors. Preclinical and clinical aspects.. Blandina, P. & Passani, M. B. (eds.). Humana Press, p. 1-49 (The Receptors; no. 28).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

Lensink, M. F., Velankar, S., Kryshtafovych, A., Huang, S. Y., Schneidman-Duhovny, D., Sali, A., Segura, J., Fernandez-Fuentes, N., Viswanath, S., Elber, R., Grudinin, S., Popov, P., Neveu, E., Lee, H., Baek, M., Park, S., Heo, L., Lee, G. R., Seok, C., Qin, S. & 82 othersZhou, H. X., Ritchie, D. W., Maigret, B., Devignes, M. D., Ghoorah, A., Torchala, M., Chaleil, R. A. G., Bates, P. A., Ben-Zeev, E., Eisenstein, M., Negi, S. S., Weng, Z., Vreven, T., Pierce, B. G., Borrman, T. M., Yu, J., Ochsenbein, F., Guerois, R., Vangone, A., Rodrigues, J. P. G. L. M., Van Zundert, G., Nellen, M., Xue, L., Karaca, E., Melquiond, A. S. J., Visscher, K., Kastritis, P. L., Bonvin, A. M. J. J., Xu, X., Qiu, L., Yan, C., Li, J., Ma, Z., Cheng, J., Zou, X., Shen, Y., Peterson, L. X., Kim, H. R., Roy, A., Han, X., Esquivel-Rodriguez, J., Kihara, D., Yu, X., Bruce, N. J., Fuller, J. C., Wade, R. C., Anishchenko, I., Kundrotas, P. J., Vakser, I. A., Imai, K., Yamada, K., Oda, T., Nakamura, T., Tomii, K., Pallara, C., Romero-Durana, M., Jiménez-García, B., Moal, I. H., Férnandez-Recio, J., Joung, J. Y., Kim, J. Y., Joo, K., Lee, J., Kozakov, D., Vajda, S., Mottarella, S., Hall, D. R., Beglov, D., Mamonov, A., Xia, B., Bohnuud, T., Del Carpio, C. A., Ichiishi, E., Marze, N., Kuroda, D., Roy Burman, S. S., Gray, J. J., Chermak, E., Cavallo, L., Oliva, R., Tovchigrechko, A. & Wodak, S. J., 2016, Proteins: Structure, Function and Bioinformatics. S1 ed. John Wiley and Sons Inc., Vol. 84. p. 323-348 26 p. (Proteins: Structure, Function and Bioinformatics; vol. 84).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Proteins
Joints
Databases

Resource transformation through alliances: The resource-based and relational rents dilemma and implications for the evolution of firm boundaries

Madhok, A., Keyhani, M., Bossink, B. A. G. & Vlaar, P. W. L., 2016, Governance Issues in Strategic Alliances. Das, T. K. (ed.). Charlotte, NC: Information Age Publishing, p. 131-150 20 p. (Research in Strategic Alliances).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

2015

Discovery of MCRs

Ruijter, E. & Orru, R. V. A., 9 Feb 2015, Multicomponent Reactions in Organic Synthesis. Wiley & Blackwell, p. 13-38 26 p. (Multicomponent Reactions in Organic Synthesis).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Geospatial Technology in Geography Education

Muniz Solari, O., Demirci, A. & van der Schee, J. A., 2015, Geospatial Technologies and Geography Education in a Changing World. Muniz Solari, O., Demirci, A. & van der Schee, J. (eds.). Tokyo: Springer, p. 1-7

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Methodologies for Effect-Directed Analysis: applications in environmental chemistry, food quality assessment and drug discovery

Jonker, L. W., Lamoree, M. H., Houtman, C. J. & Kool, J., 2015, Analyzing Biomolecular Interactions by Mass Spectrometry. Kool, J. & Niessen, W. M. A. (eds.). Germany: Wiley, p. 111-149

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Non-interacting surface solvation and dynamics in protein-protein interactions

Visscher, K. M., Kastritis, P. L. & Bonvin, A. M. J. J., 1 Mar 2015, Proteins: Structure, Function and Bioinformatics. 3 ed. John Wiley and Sons Inc., Vol. 83. p. 445-458 14 p. (Proteins: Structure, Function and Bioinformatics; vol. 83).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Proteins
Surface Properties
Protein Stability
Drug Design
Entropy

Reduced Density Matrix Functional Theory (RDMFT) and Linear Response Time-Dependent RDMFT (TD-RDMFT)

Pernal, K. & Giesbertz, K. J. H., 14 May 2015, Density-Functional Methods for Excited States. Heidelberg: Springer, Berlin, Vol. 368. p. 125-183 (Topics in Current Chemistry).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Open Access
Electrons

Synthesis of biologically relevant molecules

van Lint, M. J., Ruijter, E. & Orru, R. V. A., 24 Apr 2015, Stereoselective Multiple Bond-Forming Transformations in Organic Synthesis. Wiley, p. 393-422 30 p.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Biological Products
Catalysis
Molecules
Bioactivity
Scaffolds

The Supramolecular Organization of a Peptide-Based Nanocarrier at High Molecular Detail

Rad-Malekshahi, M., Visscher, K. M., Rodrigues, J. P. G. L. M., De Vries, R., Hennink, W. E., Baldus, M., Bonvin, A. M. J. J., Mastrobattista, E. & Weingarth, M., 24 Jun 2015, Journal of the American Chemical Society. 24 ed. American Chemical Society, Vol. 137. p. 7775-7784 10 p. (Journal of the American Chemical Society; vol. 137).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Peptides
Liposomes
Lipids
Pharmaceutical Preparations
2014

d10-ML2 Complexes: Structure, Bonding and Reactivity

Wolters, L. P. & Bickelhaupt, F. M., 2014, Structure and Bonding. Eisenstein, O. & Macgregor, S. (eds.). Berlin: Springer

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Density Functional Theory for Strongly-Interacting Electrons

Malet Giralt, F., Mirtschink, A. P., Giesbertz, K. J. H. & Gori Giorgi, P., 2014, Many-Electron Approaches in Physics, Chemistry and Mathematics. Bach, V. & Delle Site, L. (eds.). 1 ed. Switzerland: Springer, p. 153-168

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Density functional theory
Electrons
Carrier concentration

From three-dimensional GPCR structure to rational ligand discovery

Kooistra, A. J., Leurs, R., De Esch, I. J. P. & de Graaf, C., 2014, G Protein-Coupled Receptors - Modeling and Simulation. Filizola, M. (ed.). Springer New York LLC, p. 129-157 29 p. (Advances in Experimental Medicine and Biology; vol. 796).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Ligands
Screening
Workflow
Structural Models
G-Protein-Coupled Receptors

Hypervalent Carbon: Violation of the Octet Rule

Bickelhaupt, F. M., 2014, Natuurkundige Voordrachten Nieuwe Reeks 2014, 92, 63-68 (Jaarboek Koninklijke Maatschappij voor Natuurkunde Diligentia)..

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

In Vitro Toxicology Systems: Chapter 1: The Past, Present and Future of Chemical Risk Assessment

Limonciel, A. V. S., 2014, Springer Protocols. Humana Press, p. 3-23 (Methods in Pharmacology and Toxicology).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Toxicology
In Vitro Techniques

In Vitro Toxicology Systems: Chapter 20: Translational Biomarkers, In Vitro and In Vivo

Wilmes, A., Limonciel, A. V. S., Leonard, M. O. & Jennings, P., 2014, Springer Protocols. Humana Press, p. 459-478 (Methods in Pharmacology and Toxicology).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

In Vitro Toxicology Systems: Chapter 19: Stress Response Pathways

Leonard, M. O., Limonciel, A. V. S. & Jennings, P., 2014, Springer Protocols. Humana Press, p. 433-458 (Methods in Pharmacology and Toxicology).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

In Vitro Toxicology Systems: Chapter 15: Use of Induced Pluripotent Stem Cells in Drug Toxicity Screening

Rauch, C., Jennings, P. & Wilmes, A., 2014, Springer Protocols. Human Press, p. 335-350

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

In Vitro Toxicology Systems: Chapter 4: Renal cell culture

Jennings, P., Aschauer, L., Wilmes, A. & Gstraunthaler, G., 2014, Springer protocols. Humana Press, p. 79-101

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Mucin-based stationary phases as tool for the characterization of drug-mucus interaction

Gargano, A. F. G., Lämmerhofer, M., Lönn, H., Schoenmakers, P. J. & Leek, T., 18 Jul 2014, Journal of Chromatography A. Elsevier, Vol. 1351. p. 70-81 12 p. (Journal of Chromatography A; vol. 1351).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Mucins
Mucus
Drug Interactions
Pharmaceutical Preparations
Proteins

MVO-kampioen; Duurzaam vastgoed komt er wel

Bossink, B. A. G., 2014, Barometer Maatschappelijk Vastgoed. Veuger, J. (ed.). Assen: Van Gorcum, 7 p.

Research output: Chapter in Book / Report / Conference proceedingChapterProfessional

The EDA Perspective of Chemical Bonding

Bickelhaupt, F. M. & Frenking, G., 2014, The Chemical Bond - Fundamental Aspects of Chemical Bonding. Frenking, G. & Shaik, S. S. (eds.). Weinheim: Wiley-VCH, p. 121-157

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

The Use of Renal Cell Culture for Nephrotoxicity Investigations

Wilmes, A. & Jennings, P., 2014, Predictive Toxicology: From vision to reality. Wiley, Vol. 64. p. 195 126 p.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

2013

Chemoaffinity material for plasmid DNA analysis by high-performance liquid chromatography with condition-dependent switching between isoform and topoisomer selectivity

Mahut, M., Gargano, A., Schuchnigg, H., Lindner, W. & Lämmerhofer, M., 5 Mar 2013, Analytical Chemistry. 5 ed. Vol. 85. p. 2913-2920 8 p. (Analytical Chemistry; vol. 85).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Protein Isoforms
Plasmids
High Pressure Liquid Chromatography
DNA
Cinchona Alkaloids

Guanine, Xanthine and Uric Acid Assemblies: Comparative Theoretical and Experimental Studies

Paragi, G. T., Szolomajer, J., Kupihar, Z., Batta, G., Kele, Z., Padar, P., Penke, B., Zijlstra, H., Fonseca Guerra, C., Bickelhaupt, F. M. & Kovacs, L., 2013, Self-Assembled Guanosine Structures for Molecular Electronic Devices. Fritzsche, W. & Spindler, L. (eds.). Cambridge: RSC Publishing, p. 179-193

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Hyphenated Techniques, Applications of in Mass Spectrometry

Niessen, W. M. A., 2013, Elsevier Reference Module Chemical, Molecular Sciences and Engineering.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Liquid chromatography-mass spectrometry

Niessen, W. M. A., 2013, Elsevier Reference Module Chemical, Molecular Sciences and Engineering. Reedijk, J. (ed.). Elsevier

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Mass Spectrometry | Atmospheric-pressure ionization

Bruins, A. P. & Niessen, W. M. A., 2013, Elsevier Reference Module Chemical, Molecular Sciences and Engineering.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Microwave-Assisted Multicomponent Reactions in the Synthesis of Heterocycles

Kruithof, A., Ruijter, E. & Orru, R. V. A., 27 Feb 2013, Microwaves in Organic Synthesis: Third Edition. de la Hoz, A. & Loupy, A. (eds.). Weinheim: Wiley-VCH, Vol. 2. p. 1099-1171 73 p.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

MSMS and MSn

Niessen, W. M. A., 2013, Elsevier Reference Module Chemical, Molecular Sciences and Engineering.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Online Affinity Assessment and Immunoaffinity Sample Pretreatment in Capillary Electrophoresis-Mass Spectrometry

Haselberg, R. & Somsen, G. W., 1 Jan 2013, Analyzing Biomolecular Interactions by Mass Spectrometry. Wiley & Blackwell, p. 271-298 28 p.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Capillary electrophoresis
Mass spectrometry
Peptides

Solvated protein-protein docking using Kyte-Doolittle-based water preferences

Kastritis, P. L., Visscher, K. M., van Dijk, A. D. J. & Bonvin, A. M. J. J., Mar 2013, Proteins: Structure, Function and Bioinformatics. 3 ed. Vol. 81. p. 510-518 9 p. (Proteins: Structure, Function and Bioinformatics; vol. 81).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Water
Proteins
Hydrophobic and Hydrophilic Interactions
Amino Acids
Water Quality

Thermospray Ionization in Mass Spectrometry

Niessen, W. M. A., 2013, Elsevier Reference Module Chemical, Molecular Sciences and Engineering. Reedijk, J. (ed.).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

The Role of CE-MS in Metabolomics

Ramautar, R., Somsen, G. W. & de Jong, G. J., 2013, Metabolomics in Practice: Successful Strategies to Generate and Analyze Metabolic Data. Laemmerhofer, M. & Weckwerth, W. (eds.). Weinheim: Wiley-VCH, p. 177-208 32 p.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Capillary electrophoresis
Metabolomics
Capillary Electrophoresis
Mass spectrometry
Mass Spectrometry

Towards the Description of Covalent Bonds in Subsystem Density-Functional Theory

Jacob, C. R. & Visscher, L., 2013, Recent Progress in Orbital-Free Density Functional Theory. Wesolowski, T. A. & Wang, Y. A. (eds.). Singapore: World Scientific, p. 297-322 (Recent Advances in Computational Chemistry; no. 6).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic