Rebecca C Wade

Rebecca C Wade

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Rebecca C Wade

Rebecca C Wade

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100Publications

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Toward an Ensemble View of Chromatosome Structure: A Paradigm Shift from One to Many.

Structure 2018 Aug 21;26(8):1050-1057. Epub 2018 Jun 21.

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany; Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, 69120 Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany. Electronic address:

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August 2018

Estimation of Drug-Target Residence Times by τ-Random Acceleration Molecular Dynamics Simulations.

J Chem Theory Comput 2018 Jul 4;14(7):3859-3869. Epub 2018 Jun 4.

Molecular and Cellular Modeling Group , Heidelberg Institute for Theoretical Studies , Heidelberg 69118 , Germany.

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July 2018

Inter-subunit interactions drive divergent dynamics in mammalian and Plasmodium actin filaments.

PLoS Biol 2018 Jul 16;16(7):e2005345. Epub 2018 Jul 16.

Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany.

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July 2018

Impact of carbonylation on glutathione peroxidase-1 activity in human hyperglycemic endothelial cells.

Redox Biol 2018 06 1;16:113-122. Epub 2018 Mar 1.

Department of Cardiovascular Physiology, Heidelberg University, Heidelberg D-69120, Germany. Electronic address:

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June 2018

Halogen-Aromatic π Interactions Modulate Inhibitor Residence Times.

Angew Chem Int Ed Engl 2018 Jun 9;57(24):7220-7224. Epub 2018 May 9.

Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Oxford, OX3 7DQ, UK.

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June 2018

Dependence of Chromatosome Structure on Linker Histone Sequence and Posttranslational Modification.

Biophys J 2018 May 11;114(10):2363-2375. Epub 2018 May 11.

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany; Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), Heidelberg, Germany. Electronic address:

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May 2018

New approaches for computing ligand-receptor binding kinetics.

Curr Opin Struct Biol 2018 Apr 11;49:1-10. Epub 2017 Nov 11.

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany; Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany. Electronic address:

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April 2018

Comparative mapping of on-targets and off-targets for the discovery of anti-trypanosomatid folate pathway inhibitors.

Biochim Biophys Acta Gen Subj 2017 Dec 20;1861(12):3215-3230. Epub 2017 Sep 20.

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, Heidelberg 69118, Germany; Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld 282, Heidelberg 69120, Germany; Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, Heidelberg 69120, Germany. Electronic address:

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December 2017

Application of a simple quantum chemical approach to ligand fragment scoring for Trypanosoma brucei pteridine reductase 1 inhibition.

J Comput Aided Mol Des 2017 Aug 7;31(8):715-728. Epub 2017 Jul 7.

Department of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland.

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August 2017

TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets.

Nucleic Acids Res 2017 Jul;45(W1):W325-W330

Molecular and Cellular Modeling group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Baden-Württemberg 69118, Germany.

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July 2017

A unique profilin-actin interface is important for malaria parasite motility.

PLoS Pathog 2017 May 26;13(5):e1006412. Epub 2017 May 26.

Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany.

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May 2017

Comparative electrostatic analysis of adenylyl cyclase for isoform dependent regulation properties.

Proteins 2016 12 24;84(12):1844-1858. Epub 2016 Oct 24.

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany.

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December 2016

Modeling and simulation of protein-surface interactions: achievements and challenges.

Q Rev Biophys 2016 ;49:e4

Heidelberg Institute for Theoretical Studies (HITS),Schloss-Wolfsbrunnenweg 35,69118 Heidelberg,Germany.

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October 2016

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

Authors:
Marc F Lensink Sameer Velankar Andriy Kryshtafovych Shen-You Huang Dina Schneidman-Duhovny Andrej Sali Joan Segura Narcis Fernandez-Fuentes Shruthi Viswanath Ron Elber Sergei Grudinin Petr Popov Emilie Neveu Hasup Lee Minkyung Baek Sangwoo Park Lim Heo Gyu Rie Lee Chaok Seok Sanbo Qin Huan-Xiang Zhou David W Ritchie Bernard Maigret Marie-Dominique Devignes Anisah Ghoorah Mieczyslaw Torchala Raphaël A G Chaleil Paul A Bates Efrat Ben-Zeev Miriam Eisenstein Surendra S Negi Zhiping Weng Thom Vreven Brian G Pierce Tyler M Borrman Jinchao Yu Françoise Ochsenbein Raphaël Guerois Anna Vangone João P G L M Rodrigues Gydo van Zundert Mehdi Nellen Li Xue Ezgi Karaca Adrien S J Melquiond Koen Visscher Panagiotis L Kastritis Alexandre M J J Bonvin Xianjin Xu Liming Qiu Chengfei Yan Jilong Li Zhiwei Ma Jianlin Cheng Xiaoqin Zou Yang Shen Lenna X Peterson Hyung-Rae Kim Amit Roy Xusi Han Juan Esquivel-Rodriguez Daisuke Kihara Xiaofeng Yu Neil J Bruce Jonathan C Fuller Rebecca C Wade Ivan Anishchenko Petras J Kundrotas Ilya A Vakser Kenichiro Imai Kazunori Yamada Toshiyuki Oda Tsukasa Nakamura Kentaro Tomii Chiara Pallara Miguel Romero-Durana Brian Jiménez-García Iain H Moal Juan Férnandez-Recio Jong Young Joung Jong Yun Kim Keehyoung Joo Jooyoung Lee Dima Kozakov Sandor Vajda Scott Mottarella David R Hall Dmitri Beglov Artem Mamonov Bing Xia Tanggis Bohnuud Carlos A Del Carpio Eichiro Ichiishi Nicholas Marze Daisuke Kuroda Shourya S Roy Burman Jeffrey J Gray Edrisse Chermak Luigi Cavallo Romina Oliva Andrey Tovchigrechko Shoshana J Wodak

Proteins 2016 09 1;84 Suppl 1:323-48. Epub 2016 Jun 1.

Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.

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September 2016

An Efficient Low Storage and Memory Treatment of Gridded Interaction Fields for Simulations of Macromolecular Association.

J Chem Theory Comput 2016 Sep 16;12(9):4563-77. Epub 2016 Aug 16.

Heidelberg Institute for Theoretical Studies (HITS) , Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.

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September 2016

Identification of an Electrostatic Ruler Motif for Sequence-Specific Binding of Collagenase to Collagen.

J Phys Chem B 2016 08 1;120(33):8580-9. Epub 2016 Jun 1.

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies , Schloss-Wolfsbrunnenweg 35, 69117 Heidelberg, Germany.

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August 2016

Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome.

Nucleic Acids Res 2016 08 7;44(14):6599-613. Epub 2016 Jun 7.

Computational Structural Biology Laboratory, Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany Center for Multiscale Theory and Computation, Westfälische Wilhelms University, Münster 48149, Germany

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August 2016

ProSAT+: visualizing sequence annotations on 3D structure.

Protein Eng Des Sel 2016 08 9;29(8):281-4. Epub 2016 Jun 9.

Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, Heidelberg 69118, Germany Center for Molecular Biology at Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and Interdisciplinary Center for Scientific Computing (IWR), Im Neuenheimer Feld 282, Heidelberg 69120, Germany

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August 2016

Perturbation Approaches for Exploring Protein Binding Site Flexibility to Predict Transient Binding Pockets.

J Chem Theory Comput 2016 Aug 25;12(8):4100-13. Epub 2016 Jul 25.

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies , 69118 Heidelberg, Germany.

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August 2016

Structural Basis for Conserved Regulation and Adaptation of the Signal Recognition Particle Targeting Complex.

J Mol Biol 2016 07 27;428(14):2880-97. Epub 2016 May 27.

Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany. Electronic address:

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July 2016

Protein Binding Pocket Dynamics.

Acc Chem Res 2016 05 25;49(5):809-15. Epub 2016 Apr 25.

Heidelberg Institute for Theoretical Studies (HITS) , Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.

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May 2016

11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015.

Authors:
Uli Fechner Chris de Graaf Andrew E Torda Stefan Güssregen Andreas Evers Hans Matter Gerhard Hessler Nicola J Richmond Peter Schmidtke Marwin H S Segler Mark P Waller Stefanie Pleik Joan-Emma Shea Zachary Levine Ryan Mullen Karina van den Broek Matthias Epple Hubert Kuhn Andreas Truszkowski Achim Zielesny Johannes Hans Fraaije Ruben Serral Gracia Stefan M Kast Krishna C Bulusu Andreas Bender Abraham Yosipof Oren Nahum Hanoch Senderowitz Timo Krotzky Robert Schulz Gerhard Wolber Stefan Bietz Matthias Rarey Markus O Zimmermann Andreas Lange Manuel Ruff Johannes Heidrich Ionut Onlia Thomas E Exner Frank M Boeckler Marcel Bermudez Dzmitry S Firaha Oldamur Hollóczki Barbara Kirchner Christofer S Tautermann Andrea Volkamer Sameh Eid Samo Turk Friedrich Rippmann Simone Fulle Noureldin Saleh Giorgio Saladino Francesco L Gervasio Elke Haensele Lee Banting David C Whitley Jana Sopkova-de Oliveira Santos Ronan Bureau Timothy Clark Achim Sandmann Harald Lanig Patrick Kibies Jochen Heil Franziska Hoffgaard Roland Frach Julian Engel Steven Smith Debjit Basu Daniel Rauh Oliver Kohlbacher Frank M Boeckler Jonathan W Essex Michael S Bodnarchuk Gregory A Ross Arndt R Finkelmann Andreas H Göller Gisbert Schneider Tamara Husch Christoph Schütter Andrea Balducci Martin Korth Fidele Ntie-Kang Stefan Günther Wolfgang Sippl Luc Meva'a Mbaze Fidele Ntie-Kang Conrad V Simoben Lydia L Lifongo Fidele Ntie-Kang Philip Judson Jiří Barilla Miloš V Lokajíček Hana Pisaková Pavel Simr Natalia Kireeva Alexandre Petrov Denis Ostroumov Vitaly P Solovev Vladislav S Pervov Nils-Ole Friedrich Kai Sommer Matthias Rarey Johannes Kirchmair Eugen Proschak Julia Weber Daniel Moser Lena Kalinowski Janosch Achenbach Mark Mackey Tim Cheeseright Gerrit Renner Gerrit Renner Torsten C Schmidt Jürgen Schram Marion Egelkraut-Holtus Albert van Oeyen Tuomo Kalliokoski Denis Fourches Akachukwu Ibezim Chika J Mbah Umale M Adikwu Ngozi J Nwodo Alexander Steudle Brian B Masek Stephan Nagy David Baker Fred Soltanshahi Roman Dorfman Karen Dubrucq Hitesh Patel Oliver Koch Florian Mrugalla Stefan M Kast Qurrat U Ain Julian E Fuchs Robert M Owen Kiyoyuki Omoto Rubben Torella David C Pryde Robert Glen Andreas Bender Petr Hošek Vojtěch Spiwok Lewis H Mervin Ian Barrett Mike Firth David C Murray Lisa McWilliams Qing Cao Ola Engkvist Dawid Warszycki Marek Śmieja Andrzej J Bojarski Natalia Aniceto Alex Freitas Taravat Ghafourian Guido Herrmann Valentina Eigner-Pitto Alexandra Naß Rafał Kurczab Andrzej J Bojarski Andreas Lange Marcel B Günther Susanne Hennig Felix M Büttner Christoph Schall Adrian Sievers-Engler Francesco Ansideri Pierre Koch Thilo Stehle Stefan Laufer Frank M Böckler Barbara Zdrazil Floriane Montanari Gerhard F Ecker Christoph Grebner Anders Hogner Johan Ulander Karl Edman Victor Guallar Christian Tyrchan Johan Ulander Christian Tyrchan Wolfgang Klute Fredrik Bergström Christian Kramer Quoc Dat Nguyen Roland Frach Patrick Kibies Steven Strohfeldt Saraphina Böttcher Tim Pongratz Dominik Horinek Stefan M Kast Bernd Rupp Raed Al-Yamori Michael Lisurek Ronald Kühne Filipe Furtado Karina van den Broek Ludger Wessjohann Miriam Mathea Knut Baumann Siti Zuraidah Mohamad-Zobir Xianjun Fu Tai-Ping Fan Andreas Bender Maximilian A Kuhn Christoph A Sotriffer Azedine Zoufir Xitong Li Lewis Mervin Ellen Berg Mark Polokoff Wolf D Ihlenfeldt Wolf D Ihlenfeldt Jette Pretzel Zayan Alhalabi Robert Fraczkiewicz Marvin Waldman Robert D Clark Neem Shaikh Prabha Garg Alexander Kos Hans-Jürgen Himmler Achim Sandmann Christophe Jardin Heinrich Sticht Thomas B Steinbrecher Markus Dahlgren Daniel Cappel Teng Lin Lingle Wang Goran Krilov Robert Abel Richard Friesner Woody Sherman Ina A Pöhner Joanna Panecka Rebecca C Wade Stefan Bietz Karen T Schomburg Matthias Hilbig Matthias Rarey Christian Jäger Vivien Wieczorek Lance M Westerhoff Oleg Y Borbulevych Hans-Ulrich Demuth Mirko Buchholz Denis Schmidt Thomas Rickmeyer Timo Krotzky Peter Kolb Sumit Mittal Elsa Sánchez-García Mauro S Nogueira Tiago B Oliveira Fernando B da Costa Thomas J Schmidt

J Cheminform 2016 Apr 26;8(Suppl 1):18. Epub 2016 Apr 26.

Central Institute for Scientific Computing (ZISC), FAU-Erlangen-Nürnberg, Martensstr. 5a, 91058, Erlangen, Germany.

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April 2016

Ligand tunnels in T. brucei and human CYP51: Insights for parasite-specific drug design.

Biochim Biophys Acta 2016 Jan 19;1860(1 Pt A):67-78. Epub 2015 Oct 19.

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany. Electronic address:

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January 2016

On the application of the MARTINI coarse-grained model to immersion of a protein in a phospholipid bilayer.

J Chem Phys 2015 Dec;143(24):243139

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.

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December 2015

When the Label Matters: Adsorption of Labeled and Unlabeled Proteins on Charged Surfaces.

Nano Lett 2015 Nov 28;15(11):7508-13. Epub 2015 Oct 28.

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies , 69117 Heidelberg, Germany.

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November 2015

Conservation and Role of Electrostatics in Thymidylate Synthase.

Sci Rep 2015 Nov 27;5:17356. Epub 2015 Nov 27.

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.

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November 2015

A multiscale approach to simulating the conformational properties of unbound multi-C₂H₂ zinc finger proteins.

Proteins 2015 Sep 1;83(9):1604-15. Epub 2015 Jul 1.

Institute for Theoretical Physics Heidelberg University, Heidelberg, Germany.

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September 2015

SDA 7: A modular and parallel implementation of the simulation of diffusional association software.

J Comput Chem 2015 Aug 29;36(21):1631-45. Epub 2015 Jun 29.

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany.

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August 2015

Crucial HSP70 co-chaperone complex unlocks metazoan protein disaggregation.

Nature 2015 Aug 5;524(7564):247-51. Epub 2015 Aug 5.

Center for Molecular Biology of the University of Heidelberg (ZMBH), German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany.

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August 2015

webSDA: a web server to simulate macromolecular diffusional association.

Nucleic Acids Res 2015 Jul 16;43(W1):W220-4. Epub 2015 Apr 16.

Molecular and Cellular Modeling group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Baden-Württemberg, Germany Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Baden-Württemberg, Germany Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Baden-Württemberg, Germany

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July 2015

Kar1 binding to Sfi1 C-terminal regions anchors the SPB bridge to the nuclear envelope.

J Cell Biol 2015 Jun 15;209(6):843-61. Epub 2015 Jun 15.

Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany

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June 2015

On calculation of the electrostatic potential of a phosphatidylinositol phosphate-containing phosphatidylcholine lipid membrane accounting for membrane dynamics.

PLoS One 2014 20;9(8):e104778. Epub 2014 Aug 20.

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.

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May 2015

LigDig: a web server for querying ligand-protein interactions.

Bioinformatics 2015 Apr 29;31(7):1147-9. Epub 2014 Nov 29.

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Center for Molecular Biology Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Center for Molecular Biology Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Center for Molecular Biology Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Center for Molecular Biology Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany and Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany.

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April 2015

Dynamics of CYP51: implications for function and inhibitor design.

J Mol Recognit 2015 Feb 20;28(2):59-73. Epub 2015 Jan 20.

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.

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February 2015

Conformational diversity and ligand tunnels of mammalian cytochrome P450s.

Biotechnol Appl Biochem 2013 Jan-Feb;60(1):134-45

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.

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August 2014

Long range Debye-Hückel correction for computation of grid-based electrostatic forces between biomacromolecules.

BMC Biophys 2014 17;7. Epub 2014 Jun 17.

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany ; Center for Molecular Biology (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.

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July 2014

Organism-adapted specificity of the allosteric regulation of pyruvate kinase in lactic acid bacteria.

PLoS Comput Biol 2013 25;9(7):e1003159. Epub 2013 Jul 25.

Molecular and Cellular Modelling Group, Heidelberg Institute for Theoretical Studies-HITS, Heidelberg, Germany.

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February 2014

GTP regulates the microtubule nucleation activity of γ-tubulin.

Nat Cell Biol 2013 Nov 27;15(11):1317-27. Epub 2013 Oct 27.

Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), ZMBH-DKFZ Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.

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November 2013

Regulation of the activity of lactate dehydrogenases from four lactic acid bacteria.

J Biol Chem 2013 Jul 17;288(29):21295-306. Epub 2013 May 17.

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany.

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July 2013

TRAPP: a tool for analysis of transient binding pockets in proteins.

J Chem Inf Model 2013 May 16;53(5):1235-52. Epub 2013 May 16.

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.

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May 2013

Translational repression of thymidylate synthase by targeting its mRNA.

Nucleic Acids Res 2013 Apr 18;41(7):4159-70. Epub 2013 Feb 18.

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.

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April 2013

The shape of protein crowders is a major determinant of protein diffusion.

Biophys J 2013 Apr;104(7):1576-84

CellNetworks Cluster and Physikalisch-Chemisches Institut, Heidelberg University, Heidelberg, Germany.

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April 2013

Ligand-based discovery of N-(1,3-dioxo-1H,3H-benzo[de]isochromen-5-yl)-carboxamide and sulfonamide derivatives as thymidylate synthase A inhibitors.

Bioorg Med Chem Lett 2013 Feb 7;23(3):663-8. Epub 2012 Dec 7.

Dipartimento di Scienze Farmaceutiche, Università degli Studi di Modena e Reggio Emilia, Via Campi 183, 41126 Modena, Italy.

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February 2013

A tightly regulated molecular toggle controls AAA+ disaggregase.

Nat Struct Mol Biol 2012 Dec 18;19(12):1338-46. Epub 2012 Nov 18.

Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany.

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December 2012

Docking of ubiquitin to gold nanoparticles.

ACS Nano 2012 Nov 10;6(11):9863-78. Epub 2012 Oct 10.

Center S3, CNR Institute Nanoscience, Via Campi 213/A, 41125 Modena, Italy.

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November 2012

The interaction properties of the human Rab GTPase family--comparative analysis reveals determinants of molecular binding selectivity.

PLoS One 2012 16;7(4):e34870. Epub 2012 Apr 16.

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.

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August 2012

A single mutation in a tunnel to the active site changes the mechanism and kinetics of product release in haloalkane dehalogenase LinB.

J Biol Chem 2012 Aug 28;287(34):29062-74. Epub 2012 Jun 28.

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany.

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August 2012

Atomic detail brownian dynamics simulations of concentrated protein solutions with a mean field treatment of hydrodynamic interactions.

J Phys Chem B 2012 Jul 30;116(29):8523-33. Epub 2012 May 30.

Heidelberg Institute for Theoretical Studies (HITS) gGmbH, Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.

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July 2012

Multiple, ligand-dependent routes from the active site of cytochrome P450 2C9.

Curr Drug Metab 2012 Feb;13(2):143-54

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Germany.

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February 2012

Allosterically gated enzyme dynamics in the cysteine synthase complex regulate cysteine biosynthesis in Arabidopsis thaliana.

Structure 2012 Feb;20(2):292-302

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), 69118 Heidelberg, Germany.

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February 2012

The active-inactive transition of human thymidylate synthase: targeted molecular dynamics simulations.

Proteins 2011 Oct 22;79(10):2886-99. Epub 2011 Aug 22.

Heidelberg Institute for Theoretical Studies (HITS gGmbH), Heidelberg, Germany.

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October 2011

Structure and dynamics of the membrane-bound cytochrome P450 2C9.

PLoS Comput Biol 2011 Aug 11;7(8):e1002152. Epub 2011 Aug 11.

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.

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August 2011

On the structure and dynamics of the complex of the nucleosome and the linker histone.

Nucleic Acids Res 2011 Jul 25;39(12):5255-63. Epub 2011 Feb 25.

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies gGmbH, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.

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July 2011

Diffusion of hydrophobin proteins in solution and interactions with a graphite surface.

BMC Biophys 2011 Apr 21;4. Epub 2011 Apr 21.

Heidelberg Institute for Theoretical Studies (HITS) gGmbH, Schloß-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.

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April 2011

Diffusion and association processes in biological systems: theory, computation and experiment.

BMC Biophys 2011 Mar 2;4. Epub 2011 Mar 2.

Heidelberg Institute for Theoretical Studies (HITS) gGmbH, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.

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March 2011

A quantitative, real-time assessment of binding of peptides and proteins to gold surfaces.

Chemistry 2011 Jan 1;17(4):1327-36. Epub 2010 Dec 1.

Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.

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January 2011

Brownian dynamics simulation of protein solutions: structural and dynamical properties.

Biophys J 2010 Dec;99(11):3782-91

Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.

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December 2010

Structure and function of the hetero-oligomeric cysteine synthase complex in plants.

J Biol Chem 2010 Oct 18;285(43):32810-7. Epub 2010 Aug 18.

Heidelberg Institute for Plant Sciences, University of Heidelberg, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany.

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October 2010

Novel approaches for targeting thymidylate synthase to overcome the resistance and toxicity of anticancer drugs.

J Med Chem 2010 Sep;53(18):6539-49

Molecular and Cellular Modeling Group, Heidelberg Institute of Theoretical Studies gGmbH, Heidelberg, Germany.

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September 2010

Biochemical network-based drug-target prediction.

Curr Opin Biotechnol 2010 Aug 14;21(4):511-6. Epub 2010 Jun 14.

Humboldt-Universität zu Berlin, Germany.

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August 2010

Computational approaches to identifying and characterizing protein binding sites for ligand design.

J Mol Recognit 2010 Mar-Apr;23(2):209-19

Molecular and Cellular Modeling Group, EML Research, Schloss-Wolfsbrunnenweg 33, 69118 Heidelberg, Germany.

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May 2010

ProMetCS: An Atomistic Force Field for Modeling Protein-Metal Surface Interactions in a Continuum Aqueous Solvent.

J Chem Theory Comput 2010 May 16;6(5):1753-68. Epub 2010 Apr 16.

Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS gGmbH), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany, INFM-CNR National Research Center on nanoStructures and BioSystems at Surface (S3), Modena, Italy, Centre for Systems Biology, School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom, and Ludwig Maximilians University, Munich, German.

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May 2010

Comparative binding energy analysis for binding affinity and target selectivity prediction.

Proteins 2010 Jan;78(1):135-53

Molecular and Cellular Modeling Group, EML Research, Heidelberg, Germany.

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January 2010

Cross-species analysis of the glycolytic pathway by comparison of molecular interaction fields.

Mol Biosyst 2010 Jan 7;6(1):152-64. Epub 2009 Sep 7.

EML Research gGmbH, Molecular and Cellular Modelling, Schloss-Wolfsbrunnenweg 33, 69118 Heidelberg, Germany.

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January 2010

Pathways and mechanisms for product release in the engineered haloalkane dehalogenases explored using classical and random acceleration molecular dynamics simulations.

J Mol Biol 2009 Oct 3;392(5):1339-56. Epub 2009 Jul 3.

Loschmidt Laboratories, Institute of Experimental Biology and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic.

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October 2009

Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate.

Nat Chem Biol 2009 Oct 23;5(10):727-33. Epub 2009 Aug 23.

Loschmidt Laboratories, Institute of Experimental Biology and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.

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October 2009

A mechanistic model of the cysteine synthase complex.

J Mol Biol 2009 Feb 5;386(1):37-59. Epub 2008 Sep 5.

Molecular and Cell Modeling Group, EML Research, Schloss-Wolfsbrunnenweg 33, 69118 Heidelberg, Germany. anna.feldman-salit@ eml-r.villa-bosch.de

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February 2009

webPIPSA: a web server for the comparison of protein interaction properties.

Nucleic Acids Res 2008 Jul 17;36(Web Server issue):W276-80. Epub 2008 Apr 17.

Molecular and Cellular Modeling Group, EML Research gGmbH, Schloss-Wolfsbrunnenweg 33, Heidelberg, Germany.

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July 2008

On the use of PIPSA to guide target-selective drug design.

ChemMedChem 2008 Mar;3(3):413-7

EML Research GmbH, Schloss-Wolfsbrunnenweg 33, 69118 Heidelberg, Germany.

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March 2008

Calculating enzyme kinetic parameters from protein structures.

Biochem Soc Trans 2008 Feb;36(Pt 1):51-4

Molecular and Cellular Modeling Group, EML Research gGmbH, Schloss-Wolfsbrunnenweg 33, 69118 Heidelberg, Germany.

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February 2008

Mechanism of auxin interaction with Auxin Binding Protein (ABP1): a molecular dynamics simulation study.

Biophys J 2008 Jan 31;94(1):27-37. Epub 2007 Aug 31.

Ruder Bosković Institute, Zagreb, Croatia.

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January 2008

qPIPSA: relating enzymatic kinetic parameters and interaction fields.

BMC Bioinformatics 2007 Oct 5;8:373. Epub 2007 Oct 5.

Molecular and Cellular Modeling Group, EML Research gGmbH, Schloss Wolfsbrunnenweg 33, Heidelberg, 69118, Germany.

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October 2007

On the Use of Elevated Temperature in Simulations To Study Protein Unfolding Mechanisms.

J Chem Theory Comput 2007 Jul;3(4):1476-83

Molecular and Cellular Modeling Group, EML Research, Schloss-Wolfsbrunnenweg 33, 69118 Heidelberg, Germany.

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July 2007

COMBINE analysis of the specificity of binding of Ras proteins to their effectors.

Proteins 2007 May;67(2):435-47

Ruder Bosković Institute, Zagreb, Croatia.

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May 2007

Structural and electrostatic properties of ubiquitination and related pathways.

Front Biosci 2007 May 1;12:3419-30. Epub 2007 May 1.

EML Research gGmbH, Villa Bosch, Schloss-Wolfsbrunnenweg 33, 69118 Heidelberg, Germany.

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May 2007

Bridging from molecular simulation to biochemical networks.

Curr Opin Struct Biol 2007 Apr 28;17(2):166-72. Epub 2007 Mar 28.

Molecular and Cellular Modeling Group, EML Research, Schloss-Wolfsbrunnenweg 33, Heidelberg, Germany.

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April 2007

The ins and outs of cytochrome P450s.

Biochim Biophys Acta 2007 Mar 21;1770(3):390-401. Epub 2006 Jul 21.

Molecular and Cellular Modeling Group, EML Research, Schloss-Wolfsbrunnenweg 33, 69118 Heidelberg, Germany.

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March 2007

FTIR studies of the redox partner interaction in cytochrome P450: the Pdx-P450cam couple.

Biochim Biophys Acta 2007 Mar 1;1770(3):420-31. Epub 2006 Sep 1.

Max-Delbrück-Center for Molecular Medicine, Protein Dynamics Laboratory, Robert-Rössle Strasse 10, 13125 Berlin, Germany.

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March 2007

Diffusional encounter of barnase and barstar.

Biophys J 2006 Mar 16;90(6):1913-24. Epub 2005 Dec 16.

Center for Bioinformatics, Saarland University, Saarbrücken, Germany.

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March 2006

Comparison of the binding and reactivity of plant and mammalian peroxidases to indole derivatives by computational docking.

Biochemistry 2006 Mar;45(9):2940-50

Molecular Biotechnology Programme, Biomedical Center, Uppsala University School of Engineering, S-75124 Uppsala, Sweden.

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March 2006

Force Field Effects on a β-Sheet Protein Domain Structure in Thermal Unfolding Simulations.

J Chem Theory Comput 2006 Jan;2(1):140-8

Molecular and Cellular Modeling Group, EML Research, Schloss-Wolfsbrunnenweg 33, 69118 Heidelberg, Germany.

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January 2006

Multiple molecular recognition mechanisms. Cytochrome P450--a case study.

Biochim Biophys Acta 2005 Dec 16;1754(1-2):239-44. Epub 2005 Sep 16.

Molecular and Cellular Modeling Group, EML Research, Schloss-Wolfsbrunnenweg 33, 69118 Heidelberg, Germany.

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December 2005

Do mammalian cytochrome P450s show multiple ligand access pathways and ligand channelling?

EMBO Rep 2005 Jun;6(6):584-9

EML Research gGmbH, Villa Bosch, Schloss-Wolfsbrunnenweg 33, 69118 Heidelberg, Germany

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June 2005

Quantitative analysis of substrate specificity of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26.

Biochemistry 2005 Mar;44(9):3390-401

National Centre for Biomolecular Research, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic.

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March 2005