de Groot, Bert L.: search on Z-Library

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1

Ligand docking and binding site analysis with PyMOL and Autodock/Vina

Daniel Seeliger, Bert L. de Groot

Journal:

Journal of Computer-Aided Molecular Design

Year:

2010

Language:

english

File:

PDF, 676 KB

english, 2010

2

Common socio-economic cycle periods

Bert de Groot, Philip Hans Franses

Journal:

Technological Forecasting and Social Change

Year:

2012

Language:

english

File:

PDF, 231 KB

english, 2012

3

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

Huang, Jing, Rauscher, Sarah, Nawrocki, Grzegorz, Ran, Ting, Feig, Michael, de Groot, Bert L, Grubmüller, Helmut, MacKerell, Alexander D

Journal:

Year:

2016

Language:

english

File:

PDF, 450 KB

english, 2016

4

Persistent Leukocyturia and Loss of Renal Function in a Prospectively Monitored Cohort of HIV-Infected Patients Treated with Indinavir

Dieleman, Jeanne P., van Rossum, Annemarie M. C., Stricker, Bruno C. H., Sturkenboom, Miriam C. J. M., de Groot, Ronald, Telgt, Denise, Blok, Willem L., Burger, David M., Blijenberg, Bert G., Zietse,

Journal:

JAIDS Journal of Acquired Immune Deficiency Syndromes

Year:

2003

Language:

english

File:

PDF, 473 KB

english, 2003

5

Specific characteristics of speed skating

DE BOER, RUUD W., ETTEMA, GERTJAN J. C., FAESSEN, BERT G. M., KREKELS, HAN, HOLLANDER, A. PETER, GROOT, GERT DE, VAN INGEN SCHENAU, GERRIT JAN

Journal:

Medicine & Science in Sports & Exercise

Year:

1987

File:

PDF, 695 KB

1987

6

Direct knock-on of desolvated ions governs strict ion selectivity in K+ channels

Kopec, Wojciech, Köpfer, David A., Vickery, Owen N., Bondarenko, Anna S., Jansen, Thomas L. C., de Groot, Bert L., Zachariae, Ulrich

Journal:

Nature Chemistry

Year:

2018

Language:

english

File:

PDF, 3.60 MB

english, 2018

7

Partial least squares for dependent data

Singer, Marco, Krivobokova, Tatyana, Munk, Axel, de Groot, Bert

Journal:

Year:

2016

Language:

english

File:

PDF, 1.33 MB

english, 2016

8

Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset

Elisée, Eddy, Gapsys, Vytautas, Mele, Nawel, Chaput, Ludovic, Selwa, Edithe, de Groot, Bert L., Iorga, Bogdan I.

Journal:

Journal of Computer-Aided Molecular Design

Year:

2019

Language:

english

File:

PDF, 1.87 MB

english, 2019

9

Best bang for your buck: GPU nodes for GROMACS biomolecular simulations

Kutzner, Carsten, Páll, Szilárd, Fechner, Martin, Esztermann, Ansgar, de Groot, Bert L., Grubmüller, Helmut

Journal:

Journal of Computational Chemistry

Year:

2015

Language:

english

File:

PDF, 1.35 MB

english, 2015

10

Cover Picture: Nanoscale Chemical Imaging of the Reduction Behavior of a Single Catalyst Particle (Angew. Chem. Int. Ed. 20/2009)

Emiel de Smit, Ingmar Swart, J. Fredrik Creemer, Chithra Karunakaran, Drew Bertwistle, Henny W. Zandbergen, Frank M. F. de Groot, Bert M. Weckhuysen

Journal:

Angewandte Chemie International Edition

Year:

2009

Language:

english

File:

PDF, 1.04 MB

english, 2009

11

Evolution of chemokine receptors is driven by mutations in the sodium binding site

Taddese, Bruck, Deniaud, Madeline, Garnier, Antoine, Tiss, Asma, Guissouma, Hajer, Abdi, Hervé, Henrion, Daniel, Chabbert, Marie, de Groot, Bert L.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 27.34 MB

english, 2018

12

Mechanisms of Anion Conduction by Coupled Glutamate Transporters

Machtens, Jan-Philipp, Kortzak, Daniel, Lansche, Christine, Leinenweber, Ariane, Kilian, Petra, Begemann, Birgit, Zachariae, Ulrich, Ewers, David, de Groot, Bert L., Briones, Rodolfo, Fahlke, Christop

Journal:

Year:

2015

Language:

english

File:

PDF, 5.42 MB

english, 2015

13

More bang for your buck: Improved use of GPU nodes for GROMACS 2018

Kutzner, Carsten, Páll, Szilárd, Fechner, Martin, Esztermann, Ansgar, de Groot, Bert L., Grubmüller, Helmut

Journal:

Journal of Computational Chemistry

Year:

2019

Language:

english

File:

PDF, 2.34 MB

english, 2019

14

Locating the Route of Entry and Binding Sites of Benzocaine and Phenytoin in a Bacterial Voltage Gated Sodium Channel

Martin, Lewis J., Corry, Ben, de Groot, Bert L.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 3.37 MB

english, 2014

15

Glypican 3 Overexpression across a Broad Spectrum of Tumor Types Discovered with Functional Genomic mRNA Profiling of a Large Cancer Database

Moek, Kirsten L., Fehrmann, Rudolf S.N., van der Vegt, Bert, de Vries, Elisabeth G.E., de Groot, Derk Jan A.

Journal:

The American Journal of Pathology

Year:

2018

Language:

english

File:

PDF, 2.09 MB

english, 2018

16

A single NaK channel conformation is not enough for non-selective ion conduction

Shi, Chaowei, He, Yao, Hendriks, Kitty, de Groot, Bert L., Cai, Xiaoying, Tian, Changlin, Lange, Adam, Sun, Han

Journal:

Nature Communications

Year:

2018

Language:

english

File:

PDF, 1.50 MB

english, 2018

17

Quantitative ultrasound of the tongue and submental muscles in children and young adults

Lenie Van Den Engel-Hoek, Nens Van Alfen, Bert J.M. De Swart, Imelda J.M. De Groot, Sigrid Pillen

Journal:

Year:

2012

Language:

english

File:

PDF, 328 KB

english, 2012

18

X-ray nanoscopy of cobalt Fischer–Tropsch catalysts at work

Cats, Korneel H., Gonzalez-Jimenez, Ines D., Liu, Yijin, Nelson, Johanna, van Campen, Douglas, Meirer, Florian, van der Eerden, Ad M. J., de Groot, Frank M. F., Andrews, Joy C., Weckhuysen, Bert M.

Journal:

Chemical Communications

Year:

2013

Language:

english

File:

PDF, 1.66 MB

english, 2013

19

Stability through cycles

Bert de Groot, Philip Hans Franses

Journal:

Technological Forecasting and Social Change

Year:

2008

Language:

english

File:

PDF, 454 KB

english, 2008

20

Cycles in basic innovations

Bert de Groot, Philip Hans Franses

Journal:

Technological Forecasting and Social Change

Year:

2009

Language:

english

File:

PDF, 290 KB

english, 2009

21

A Non-canonical Voltage-Sensing Mechanism Controls Gating in K2P K+ Channels

Schewe, Marcus, Nematian-Ardestani, Ehsan, Sun, Han, Musinszki, Marianne, Cordeiro, Sönke, Bucci, Giovanna, de Groot, Bert L., Tucker, Stephen J., Rapedius, Markus, Baukrowitz, Thomas

Journal:

Year:

2016

Language:

english

File:

PDF, 4.62 MB

english, 2016

22

Behavioral performance, brain histology, and EEG sequela after immediate combined atropine/diazepam treatment of soman-intoxicated rats

Ingrid H.C.H.M. Philippens, Bert P.C. Melchers, Didima M.G. De Groot, Otto L. Wolthuis

Journal:

Pharmacology Biochemistry and Behavior

Year:

1992

Language:

english

File:

PDF, 953 KB

english, 1992

23

The Atomistic Mechanism of Conformational Transition in Adenylate Kinase: A TEE-REX Molecular Dynamics Study

Marcus B. Kubitzki, Bert L. de Groot

Journal:

Year:

2008

Language:

english

File:

PDF, 1.11 MB

english, 2008

24

Does CO2 Permeate through Aquaporin-1?

Hub, Jochen S., de Groot, Bert L.

Journal:

Biophysical Journal

Year:

2006

Language:

english

File:

PDF, 1.31 MB

english, 2006

25

How the Dynamics of the Metal-Binding Loop Region Controls the Acid Transition in Cupredoxins

Paltrinieri, Licia, Borsari, Marco, Battistuzzi, Gianantonio, Sola, Marco, Dennison, Christopher, de Groot, Bert L., Corni, Stefano, Bortolotti, Carlo Augusto

Journal:

Year:

2013

Language:

english

File:

PDF, 2.17 MB

english, 2013

26

Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field

Rauscher, Sarah, Gapsys, Vytautas, Volkhardt, Andreas, Blau, Christian, de Groot, Bert L., Grubmüller, Helmut

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 40 KB

english, 2014

27

1s2p Resonant Inelastic X-ray Scattering of Iron Oxides

de Groot, Frank M. F., Glatzel, Pieter, Bergmann, Uwe, van Aken, Peter A., Barrea, Raul A., Klemme, Stephan, Hävecker, Michael, Knop-Gericke, Axel, Heijboer, Willem M., Weckhuysen, Bert M.

Journal:

Journal of Physical Chemistry B

Year:

2005

Language:

english

File:

PDF, 698 KB

english, 2005

28

Do commercial real estate prices have predictive content for GDP?

Franses, Philip Hans, De Groot, Bert

Journal:

Applied Economics

Year:

2013

Language:

english

File:

PDF, 381 KB

english, 2013

29

Effects of Prenatal Exposure to Betamethasone and Indomethacin on the Glomerular Filtration Rate in the Preterm Infant

van den Anker, John N, Hop, Wim C J, de Groot, Ronald, van der Heijden, Bert J, Broerse, Henriette M, Lindemans, Jan, Sauer, Pieter J J

Journal:

Pediatric Research

Year:

1994

Language:

english

File:

PDF, 475 KB

english, 1994

30

CHARMM36: An Improved Force Field for Folded and Intrinsically Disordered Proteins

Huang, Jing, Rauscher, Sarah, Nawrocki, Grzegorz, Ran, Ting, Feig, Michael, de Groot, Bert L., Grubmüller, Helmut, MacKerell, Alexander D.

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 69 KB

english, 2017

31

Role of Pore-Lining Residues in Defining the Rate of Water Conduction by Aquaporin-0

Saboe, Patrick O., Rapisarda, Chiara, Kaptan, Shreyas, Hsiao, Yu-Shan, Summers, Samantha R., De Zorzi, Rita, Dukovski, Danijela, Yu, Jiaheng, de Groot, Bert L., Kumar, Manish, Walz, Thomas

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 2.17 MB

english, 2017

32

Temperature dependence of protein-water interactions in a gated yeast aquaporin

Aponte-Santamaría, Camilo, Fischer, Gerhard, Båth, Petra, Neutze, Richard, de Groot, Bert L.

Journal:

Scientific Reports

Year:

2017

Language:

english

File:

PDF, 3.76 MB

english, 2017

33

Resolving the atomistic modes of anle138b inhibitory action on peptide oligomer formation.

Matthes, Dirk, Gapsys, Vytautas, Griesinger, Christian, de Groot, Bert L.

Journal:

ACS Chemical Neuroscience

Year:

2017

Language:

english

File:

PDF, 5.71 MB

english, 2017

34

Utilizing dipole-dipole cross-correlated relaxation for the measurement of angles between pairs of opposing CαHα-CαHα bonds in anti-parallel β-sheets

Sabo, T. Michael, Gapsys, Vytautas, Walter, Korvin F.A., Fenwick, R. Bryn, Becker, Stefan, Salvatella, Xavier, de Groot, Bert L., Lee, Donghan, Griesinger, Christian

Journal:

Year:

2018

Language:

english

File:

PDF, 2.76 MB

english, 2018

35

Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset

Elisée, Eddy, Gapsys, Vytautas, Mele, Nawel, Chaput, Ludovic, Selwa, Edithe, de Groot, Bert L., Iorga, Bogdan I.

Journal:

Journal of Computer-Aided Molecular Design

Year:

2019

File:

PDF, 1.87 MB

2019

36

The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations

Rizzi, Andrea, Jensen, Travis, Slochower, David R., Aldeghi, Matteo, Gapsys, Vytautas, Ntekoumes, Dimitris, Bosisio, Stefano, Papadourakis, Michail, Henriksen, Niel M., de Groot, Bert L., Cournia, Zoe

Journal:

Journal of Computer-Aided Molecular Design

Year:

2020

File:

PDF, 4.04 MB

2020

37

Nanoscale Chemical Imaging of the Reduction Behavior of a Single Catalyst Particle

Emiel de Smit, Ingmar Swart, J. Fredrik Creemer, Chithra Karunakaran, Drew Bertwistle, Henny W. Zandbergen, Frank M. F. de Groot, Bert M. Weckhuysen

Journal:

Angewandte Chemie International Edition

Year:

2009

Language:

english

File:

PDF, 712 KB

english, 2009

38

In-situ Scanning Transmission X-Ray Microscopy of Catalytic Solids and Related Nanomaterials

Frank M. F. de Groot, Emiel de Smit, Matti M. van Schooneveld, Luis R. Aramburo, Bert M. Weckhuysen

Journal:

Year:

2010

Language:

english

File:

PDF, 939 KB

english, 2010

39

Acyl chain order parameter profiles in phospholipid bilayers: computation from molecular dynamics simulations and comparison with2H NMR experiments

Louic S. Vermeer, Bert L. de Groot, Valérie Réat, Alain Milon, Jerzy Czaplicki

Journal:

European Biophysics Journal

Year:

2007

Language:

english

File:

PDF, 403 KB

english, 2007

40

Induction of cytochrome P-450 b, e-type isozymes by polychlorionated biphenyls in rat liver : Molecular cloning of induced mRNAs

Bob J. SCHOLTE, Bert te VELDE, Gert S. P. GROOT, John de VRIES

Journal:

Year:

1985

Language:

english

File:

PDF, 1.08 MB

english, 1985

41

The role of Cu on the reduction behavior and surface properties of Fe-based Fischer–Tropsch catalysts

de Smit, Emiel, de Groot, Frank M. F., Blume, Raoul, Hävecker, Michael, Knop-Gericke, Axel, Weckhuysen, Bert M.

Journal:

Physical Chemistry Chemical Physics

Year:

2009

Language:

english

File:

PDF, 1.09 MB

english, 2009

42

Outcome analysis of major cardiac operations in low weight neonates

Thierry Bové, Katrien François, Katya De Groote, Bert Suys, Daniel De Wolf, Hendrik Verhaaren, Dirk Matthys, Annelies Moerman, Jan Poelaert, Piet Vanhaesebroeck, Guido Van Nooten

Journal:

The Annals of Thoracic Surgery

Year:

2004

Language:

english

File:

PDF, 146 KB

english, 2004

43

Ubiquitin Dynamics in Complexes Reveal Molecular Recognition Mechanisms Beyond Induced Fit and Conformational Selection

Peters, Jan H., de Groot, Bert L., Levitt, Michael

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.67 MB

english, 2012

44

Secondary Structure Propensities in Peptide Folding Simulations: A Systematic Comparison of Molecular Mechanics Interaction Schemes

Matthes, Dirk, de Groot, Bert L.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 1.02 MB

english, 2009

45

Phosphorylation Drives a Dynamic Switch in Serine/Arginine-Rich Proteins

Xiang, ShengQi, Gapsys, Vytautas, Kim, Hai-Young, Bessonov, Sergey, Hsiao, He-Hsuan, Möhlmann, Sina, Klaukien, Volker, Ficner, Ralf, Becker, Stefan, Urlaub, Henning, Lührmann, Reinhard, de Groot, Bert

Journal:

Year:

2013

Language:

english

File:

PDF, 3.75 MB

english, 2013

46

Conformational Transitions Upon Ligand Binding: Holo Structure Prediction from Apo Conformations

Seeliger, Daniel, de Groot, Bert L.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 34 KB

english, 2010

47

Do Male Mice Prefer or Avoid Each Other's Company? Influence of Hierarchy, Kinship, and Familiarity

Van Loo, Pascalle L. P., de Groot, Arco C., Van Zutphen, Bert F. M., Baumans, Vera

Journal:

Journal of Applied Animal Welfare Science

Year:

2001

Language:

english

File:

PDF, 229 KB

english, 2001

48

pmx: Automated protein structure and topology generation for alchemical perturbations

Gapsys, Vytautas, Michielssens, Servaas, Seeliger, Daniel, de Groot, Bert L.

Journal:

Journal of Computational Chemistry

Year:

2015

Language:

english

File:

PDF, 490 KB

english, 2015

49

Testing for harmonic regressors

Franses, Philip Hans, de Groot, Bert, Legerstee, Rianne

Journal:

Journal of Applied Statistics

Year:

2009

Language:

english

File:

PDF, 124 KB

english, 2009

50

Insights into the function of ion channels by computational electrophysiology simulations

Kutzner, Carsten, Köpfer, David A., Machtens, Jan-Philipp, de Groot, Bert L., Song, Chen, Zachariae, Ulrich

Journal:

Biochimica et Biophysica Acta (BBA) - Biomembranes

Year:

2016

Language:

english

File:

PDF, 5.13 MB

english, 2016

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