Daan P. Geerke

4.4k total citations · 2 hit papers
67 papers, 3.4k citations indexed

About

Daan P. Geerke is a scholar working on Molecular Biology, Atomic and Molecular Physics, and Optics and Computational Theory and Mathematics. According to data from OpenAlex, Daan P. Geerke has authored 67 papers receiving a total of 3.4k indexed citations (citations by other indexed papers that have themselves been cited), including 37 papers in Molecular Biology, 20 papers in Atomic and Molecular Physics, and Optics and 17 papers in Computational Theory and Mathematics. Recurrent topics in Daan P. Geerke's work include Protein Structure and Dynamics (22 papers), Computational Drug Discovery Methods (17 papers) and Spectroscopy and Quantum Chemical Studies (15 papers). Daan P. Geerke is often cited by papers focused on Protein Structure and Dynamics (22 papers), Computational Drug Discovery Methods (17 papers) and Spectroscopy and Quantum Chemical Studies (15 papers). Daan P. Geerke collaborates with scholars based in Netherlands, United States and Germany. Daan P. Geerke's co-authors include Wilfred F. van Gunsteren, Chris Oostenbrink, Alan E. Mark, Philippe H. Hünenberger, Alpeshkumar K. Malde, Haibo Yu, Nico Vermeulen, Dirk Bakowies, Mika A. Kastenholz and Markus Christen and has published in prestigious journals such as Journal of the American Chemical Society, Angewandte Chemie International Edition and Nature Communications.

In The Last Decade

Daan P. Geerke

66 papers receiving 3.4k citations

Hit Papers

align trajectories

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

The GROMOS software for biomolecular simulation: GROMOS05

2005 512 citations Daan P. Geerke, Wilfred F. van Gunsteren et al. Journal of Computational Chemistry profile →
Automated Topology Builder Version 3.0: Prediction of Solvation Free Enthalpies in Water and Hexane

2018 398 citations Martin Stroet, Bertrand Caron et al. profile →

Peers — A (Enhanced Table)

Peers by citation overlap · career bar shows stage (early→late) cites · hero ref

Name	h						Papers	Cites
Daan P. Geerke Netherlands	29	1.9k	858	650	487	449	67	3.4k
Yujie Wu China	22	2.0k 1.1×	1.0k 1.2×	712 1.1×	655 1.3×	788 1.8×	46	4.2k
Felice C. Lightstone United States	32	2.2k 1.2×	463 0.5×	500 0.8×	733 1.5×	661 1.5×	105	3.9k
Danilo Roccatano Germany	37	2.3k 1.2×	519 0.6×	756 1.2×	495 1.0×	218 0.5×	97	3.7k
Romelia Salomón–Ferrer United States	11	3.7k 2.0×	576 0.7×	900 1.4×	495 1.0×	690 1.5×	17	5.3k
Richard H. Henchman United Kingdom	30	2.3k 1.2×	1.2k 1.4×	801 1.2×	421 0.9×	557 1.2×	65	4.1k
Vı́ctor Guallar Spain	42	3.5k 1.8×	718 0.8×	917 1.4×	674 1.4×	569 1.3×	192	6.4k
Michel A. Cuendet Switzerland	22	2.1k 1.1×	383 0.4×	490 0.8×	577 1.2×	639 1.4×	54	4.0k
Pekka Mark Sweden	9	1.9k 1.0×	473 0.6×	581 0.9×	460 0.9×	545 1.2×	11	3.8k

Countries citing papers authored by Daan P. Geerke

Since Specialization

Citations

This map shows the geographic impact of Daan P. Geerke's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Daan P. Geerke with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Daan P. Geerke more than expected).

Fields of papers citing papers by Daan P. Geerke

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Daan P. Geerke. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Daan P. Geerke. The network helps show where Daan P. Geerke may publish in the future.

Co-authorship network of co-authors of Daan P. Geerke

This figure shows the co-authorship network connecting the top 25 collaborators of Daan P. Geerke. A scholar is included among the top collaborators of Daan P. Geerke based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with Daan P. Geerke. Daan P. Geerke is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

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20 of 20 papers shown

Schreuder, Mark, Georges Jourdi, David A. Poole, et al.. (2024). Minimally modified human blood coagulation factor X to bypass direct factor Xa inhibitors. Journal of Thrombosis and Haemostasis. 22(8). 2211–2226. 1 indexed citations

Stroet, Martin, Bertrand Caron, Marc van Dijk, et al.. (2023). OFraMP: a fragment-based tool to facilitate the parametrization of large molecules. Journal of Computer-Aided Molecular Design. 37(8). 357–371. 11 indexed citations

Vries, Ida de, Tatjana Heidebrecht, Patrick H. N. Celie, et al.. (2023). Distant sequence regions of JBP1 contribute to J-DNA binding. Life Science Alliance. 6(9). e202302150–e202302150.

Haan, Cornelis A. M. de, et al.. (2022). An Efficient, Site‐Selective and Spontaneous Peptide Macrocyclisation During in vitro Translation. Chemistry - A European Journal. 29(14). e202203923–e202203923. 8 indexed citations

Geerke, Daan P., et al.. (2020). Polarisable force fields: what do they add in biomolecular simulations?. Current Opinion in Structural Biology. 61. 182–190. 65 indexed citations

Cascioferro, Stella, Giovanna Li Petri, Barbara Parrino, et al.. (2020). Imidazo[2,1-b] [1,3,4]thiadiazoles with antiproliferative activity against primary and gemcitabine-resistant pancreatic cancer cells. European Journal of Medicinal Chemistry. 189. 112088–112088. 58 indexed citations

Dijk, Marc van, et al.. (2020). Recent Developments in Linear Interaction Energy Based Binding Free Energy Calculations. Frontiers in Molecular Biosciences. 7. 114–114. 23 indexed citations

Caron, Bertrand, et al.. (2019). Automated partial atomic charge assignment for drug-like molecules: a fast knapsack approach. Algorithms for Molecular Biology. 14(1). 1–1. 10 indexed citations

Visscher, Koen, et al.. (2017). Engineered factor Xa variants retain procoagulant activity independent of direct factor Xa inhibitors. Nature Communications. 8(1). 35 indexed citations

10.

Geerke, Daan P., et al.. (2017). Engineering a self-sufficient Mycobacterium tuberculosis CYP130 by gene fusion with the reductase-domain of CYP102A1 from Bacillus megaterium. Journal of Inorganic Biochemistry. 180. 47–53. 8 indexed citations

11.

Capoferri, Luigi, et al.. (2017). eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations. Journal of Cheminformatics. 9(1). 58–58. 7 indexed citations

12.

Capoferri, Luigi, et al.. (2016). Improving the iterative Linear Interaction Energy approach using automated recognition of configurational transitions. Journal of Molecular Modeling. 22(1). 31–31. 10 indexed citations

13.

Capoferri, Luigi, et al.. (2015). Linear Interaction Energy Based Prediction of Cytochrome P450 1A2 Binding Affinities with Reliability Estimation. PLoS ONE. 10(11). e0142232–e0142232. 19 indexed citations

14.

Sanz, Ferrán, Luigi Capoferri, Nico Vermeulen, et al.. (2015). Integrative Modeling Strategies for Predicting Drug Toxicities at the eTOX Project. Molecular Informatics. 34(6-7). 477–484. 10 indexed citations

15.

Capoferri, Luigi, et al.. (2014). Application of engineered cytochrome P450 mutants as biocatalysts for the synthesis of benzylic and aromatic metabolites of fenamic acid NSAIDs. Bioorganic & Medicinal Chemistry. 22(20). 5613–5620. 33 indexed citations

16.

Guerra, Célia Fonseca, et al.. (2012). The Role of Protein Plasticity in Computational Rationalization Studies on Regioselectivity in Testosterone Hydroxylation by Cytochrome P450 BM3 Mutants. Current Drug Metabolism. 13(2). 155–166. 9 indexed citations

17.

Geerke, Daan P., et al.. (2008). On the direct calculation of the free energy of quantization for molecular systems in the condensed phase. Journal of Computational Chemistry. 30(4). 514–523. 7 indexed citations

18.

Geerke, Daan P., Stephan Thiel, Walter Thiel, & Wilfred F. van Gunsteren. (2007). QM–MM interactions in simulations of liquid water using combined semi-empirical/classical Hamiltonians. Physical Chemistry Chemical Physics. 10(2). 297–302. 19 indexed citations

19.

Geerke, Daan P. & Wilfred F. van Gunsteren. (2006). Force Field Evaluation for Biomolecular Simulation: Free Enthalpies of Solvation of Polar and Apolar Compounds in Various Solvents. ChemPhysChem. 7(3). 671–678. 32 indexed citations

20.

Jong, G. Theodoor de, Daan P. Geerke, Axel Diefenbach, Miquel Solà, & F. Matthias Bickelhaupt. (2005). Oxidative addition of the ethane CC bond to Pd. An ab initio benchmark and DFT validation study. Journal of Computational Chemistry. 26(10). 1006–1020. 66 indexed citations

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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