Daria B Kokh

Affiliations

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

ORCID: 0000000246876572

Publications (16)

A workflow for exploring ligand dissociation from a macromolecule: Efficient random acceleration molecular dynamics simulation and interaction fingerprint analysis of ligand trajectories.

The Journal of chemical physics

Avec: Daria B Kokh , Bernd Doser , Stefan Richter , Fabian Ormersbach , Xingyi Cheng , Rebecca C Wade

Computational screening of the effects of mutations on protein-protein off-rates and dissociation mechanisms by τRAMD.

Communications biology

Avec: Giulia D'Arrigo , Daria B Kokh , Ariane Nunes-Alves , Rebecca C Wade

Machine Learning Analysis of τRAMD Trajectories to Decipher Molecular Determinants of Drug-Target Residence Times.

Frontiers in molecular biosciences

Avec: Daria B Kokh , Tom Kaufmann , Bastian Kister , Rebecca C Wade

Graphene BioFET sensors for SARS-CoV-2 detection: a multiscale simulation approach.

Nanoscale advances

Avec: A Toral-Lopez , D B Kokh , E G Marin , R C Wade , A Godoy

Molecular Dynamics Simulations of the Human Ecto-5'-Nucleotidase (h-ecto-5'-NT, CD73): Insights into Protein Flexibility and Binding Site Dynamics.

Journal of chemical information and modeling

Avec: Lucas G Viviani , Daria B Kokh , Rebecca C Wade , Antonia T-do Amaral

Oncologic Outcomes for Different Axillary Staging Techniques in Patients with Nodal-Positive Breast Cancer Undergoing Neoadjuvant Systematic Treatment: A Cancer Registry Study.

Annals of surgical oncology

Avec: André Pfob , Daria B Kokh , Irina Surovtsova , Fabian Riedel , Philipp Morakis , Joerg Heil

Use of chemotherapy and loco-regional therapy in stage IA triple-negative breast cancer and their association with oncologic outcomes: A cancer registry study.

International journal of cancer

Avec: André Pfob , Irina Surovtsova , Daria B Kokh , Auteur inconnu , Joerg Heil , Maggie Banys-Paluchowski , Philipp Morakis

G Protein-Coupled Receptor-Ligand Dissociation Rates and Mechanisms from τRAMD Simulations.

Journal of chemical theory and computation

Avec: Daria B Kokh , Rebecca C Wade

Ligand unbinding mechanisms and kinetics for T4 lysozyme mutants from τRAMD simulations.

Current research in structural biology

Avec: Ariane Nunes-Alves , Daria B Kokh , Rebecca C Wade

Druggability Assessment in TRAPP Using Machine Learning Approaches.

Journal of chemical information and modeling

Avec: Jui-Hung Yuan , Sungho Bosco Han , Stefan Richter , Rebecca C Wade , Daria B Kokh

Brownian Dynamics Simulations of Proteins in the Presence of Surfaces: Long-Range Electrostatics and Mean-Field Hydrodynamics.

Journal of chemical theory and computation

Avec: Martin Reinhardt , Neil J Bruce , Daria B Kokh , Rebecca C Wade

A Blueprint for High Affinity SARS-CoV-2 Mpro Inhibitors from Activity-Based Compound Library Screening Guided by Analysis of Protein Dynamics.

ACS pharmacology & translational science

Avec: Jonas Gossen , Simone Albani , Anton Hanke , Benjamin P Joseph , Cathrine Bergh , Maria Kuzikov , Elisa Costanzi , Candida Manelfi , Paola Storici , Philip Gribbon , Andrea R Beccari , Carmine Talarico , Francesca Spyrakis , Erik Lindahl , Andrea Zaliani , Paolo Carloni , Rebecca C Wade , Francesco Musiani , Daria B Kokh , Giulia Rossetti

Recent progress in molecular simulation methods for drug binding kinetics.

Current opinion in structural biology

Avec: Ariane Nunes-Alves , Daria B Kokh , Rebecca C Wade

Contact Map Fingerprints of Protein-Ligand Unbinding Trajectories Reveal Mechanisms Determining Residence Times Computed from Scaled Molecular Dynamics.

Journal of chemical theory and computation

Avec: Marc Bianciotto , Paraskevi Gkeka , Daria B Kokh , Rebecca C Wade , Hervé Minoux

Structure-kinetic relationship reveals the mechanism of selectivity of FAK inhibitors over PYK2.

Cell chemical biology

Avec: Benedict-Tilman Berger , Marta Amaral , Daria B Kokh , Ariane Nunes-Alves , Djordje Musil , Timo Heinrich , Martin Schröder , Rebecca Neil , Jing Wang , Iva Navratilova , Joerg Bomke , Jonathan M Elkins , Susanne Müller , Matthias Frech , Rebecca C Wade , Stefan Knapp

A community effort in SARS-CoV-2 drug discovery.

Molecular informatics

Avec: Johannes Schimunek , Philipp Seidl , Katarina Elez , Tim Hempel , Tuan Le , Frank Noé , Simon Olsson , Lluís Raich , Robin Winter , Hatice Gokcan , Filipp Gusev , Evgeny M Gutkin , Olexandr Isayev , Maria G Kurnikova , Chamali H Narangoda , Roman Zubatyuk , Ivan P Bosko , Konstantin V Furs , Anna D Karpenko , Yury V Kornoushenko , Mikita Shuldau , Artsemi Yushkevich , Mohammed B Benabderrahmane , Patrick Bousquet-Melou , Ronan Bureau , Beatrice Charton , Bertrand C Cirou , Gérard Gil , William J Allen , Suman Sirimulla , Stanley Watowich , Nick Antonopoulos , Nikolaos Epitropakis , Agamemnon Krasoulis , Vassilis Itsikalis , Stavros Theodorakis , Igor Kozlovskii , Anton Maliutin , Alexander Medvedev , Petr Popov , Mark Zaretckii , Hamid Eghbal-Zadeh , Christina Halmich , Sepp Hochreiter , Andreas Mayr , Peter Ruch , Michael Widrich , Francois Berenger , Ashutosh Kumar , Yoshihiro Yamanishi , Kam Y J Zhang , Emmanuel Bengio , Yoshua Bengio , Moksh J Jain , Maksym Korablyov , Cheng-Hao Liu , Gilles Marcou , Enrico Glaab , Kelly Barnsley , Suhasini M Iyengar , Mary Jo Ondrechen , V Joachim Haupt , Florian Kaiser , Michael Schroeder , Luisa Pugliese , Simone Albani , Christina Athanasiou , Andrea Beccari , Paolo Carloni , Giulia D'Arrigo , Eleonora Gianquinto , Jonas Goßen , Anton Hanke , Benjamin P Joseph , Daria B Kokh , Sandra Kovachka , Candida Manelfi , Goutam Mukherjee , Abraham Muñiz-Chicharro , Francesco Musiani , Ariane Nunes-Alves , Giulia Paiardi , Giulia Rossetti , S Kashif Sadiq , Francesca Spyrakis , Carmine Talarico , Alexandros Tsengenes , Rebecca C Wade , Conner Copeland , Jeremiah Gaiser , Daniel R Olson , Amitava Roy , Vishwesh Venkatraman , Travis J Wheeler , Haribabu Arthanari , Klara Blaschitz , Marco Cespugli , Vedat Durmaz , Konstantin Fackeldey , Patrick D Fischer , Christoph Gorgulla , Christian Gruber , Karl Gruber , Michael Hetmann , Jamie E Kinney , Krishna M Padmanabha Das , Shreya Pandita , Amit Singh , Georg Steinkellner , Guilhem Tesseyre , Gerhard Wagner , Zi-Fu Wang , Ryan J Yust , Dmitry S Druzhilovskiy , Dmitry A Filimonov , Pavel V Pogodin , Vladimir Poroikov , Anastassia V Rudik , Leonid A Stolbov , Alexander V Veselovsky , Maria De Rosa , Giada De Simone , Maria R Gulotta , Jessica Lombino , Nedra Mekni , Ugo Perricone , Arturo Casini , Amanda Embree , D Benjamin Gordon , David Lei , Katelin Pratt , Christopher A Voigt , Kuang-Yu Chen , Yves Jacob , Tim Krischuns , Pierre Lafaye , Agnès Zettor , M Luis Rodríguez , Kris M White , Daren Fearon , Frank Von Delft , Martin A Walsh , Dragos Horvath , Charles L Brooks , Babak Falsafi , Bryan Ford , Adolfo García-Sastre , Sang Yup Lee , Nadia Naffakh , Alexandre Varnek , Günter Klambauer , Thomas M Hermans

Réseau de co-auteurs

Rebecca C Wade 13 collaborations

Ariane Nunes-Alves 5 collaborations

Stefan Richter 2 collaborations

Giulia D'Arrigo 2 collaborations

André Pfob 2 collaborations

Irina Surovtsova 2 collaborations

Philipp Morakis 2 collaborations

Joerg Heil 2 collaborations

Simone Albani 2 collaborations

Anton Hanke 2 collaborations

Benjamin P Joseph 2 collaborations

Candida Manelfi 2 collaborations

Carmine Talarico 2 collaborations

Francesca Spyrakis 2 collaborations

Paolo Carloni 2 collaborations

Francesco Musiani 2 collaborations

Giulia Rossetti 2 collaborations

Bernd Doser 1 collaboration

Fabian Ormersbach 1 collaboration

Xingyi Cheng 1 collaboration

Tom Kaufmann 1 collaboration

Bastian Kister 1 collaboration

A Toral-Lopez 1 collaboration

D B Kokh 1 collaboration

E G Marin 1 collaboration

R C Wade 1 collaboration

A Godoy 1 collaboration

Lucas G Viviani 1 collaboration

Antonia T-do Amaral 1 collaboration

Fabian Riedel 1 collaboration

None None 1 collaboration

Maggie Banys-Paluchowski 1 collaboration

Jui-Hung Yuan 1 collaboration

Sungho Bosco Han 1 collaboration

Martin Reinhardt 1 collaboration

Neil J Bruce 1 collaboration

Jonas Gossen 1 collaboration

Cathrine Bergh 1 collaboration

Maria Kuzikov 1 collaboration

Elisa Costanzi 1 collaboration

Paola Storici 1 collaboration

Philip Gribbon 1 collaboration

Andrea R Beccari 1 collaboration

Erik Lindahl 1 collaboration

Andrea Zaliani 1 collaboration

Marc Bianciotto 1 collaboration

Paraskevi Gkeka 1 collaboration

Hervé Minoux 1 collaboration

Benedict-Tilman Berger 1 collaboration

Marta Amaral 1 collaboration

Djordje Musil 1 collaboration

Timo Heinrich 1 collaboration

Martin Schröder 1 collaboration

Rebecca Neil 1 collaboration

Jing Wang 1 collaboration

Iva Navratilova 1 collaboration

Joerg Bomke 1 collaboration

Jonathan M Elkins 1 collaboration

Susanne Müller 1 collaboration

Matthias Frech 1 collaboration

Stefan Knapp 1 collaboration

Johannes Schimunek 1 collaboration

Philipp Seidl 1 collaboration

Katarina Elez 1 collaboration

Tim Hempel 1 collaboration

Tuan Le 1 collaboration

Frank Noé 1 collaboration

Simon Olsson 1 collaboration

Lluís Raich 1 collaboration

Robin Winter 1 collaboration

Hatice Gokcan 1 collaboration

Filipp Gusev 1 collaboration

Evgeny M Gutkin 1 collaboration

Olexandr Isayev 1 collaboration

Maria G Kurnikova 1 collaboration

Chamali H Narangoda 1 collaboration

Roman Zubatyuk 1 collaboration

Ivan P Bosko 1 collaboration

Konstantin V Furs 1 collaboration

Anna D Karpenko 1 collaboration

Yury V Kornoushenko 1 collaboration

Mikita Shuldau 1 collaboration

Artsemi Yushkevich 1 collaboration

Mohammed B Benabderrahmane 1 collaboration

Patrick Bousquet-Melou 1 collaboration

Ronan Bureau 1 collaboration

Beatrice Charton 1 collaboration

Bertrand C Cirou 1 collaboration

Gérard Gil 1 collaboration

William J Allen 1 collaboration

Suman Sirimulla 1 collaboration

Stanley Watowich 1 collaboration

Nick Antonopoulos 1 collaboration

Nikolaos Epitropakis 1 collaboration

Agamemnon Krasoulis 1 collaboration

Vassilis Itsikalis 1 collaboration

Stavros Theodorakis 1 collaboration

Igor Kozlovskii 1 collaboration

Anton Maliutin 1 collaboration

Alexander Medvedev 1 collaboration

Petr Popov 1 collaboration

Mark Zaretckii 1 collaboration

Hamid Eghbal-Zadeh 1 collaboration

Christina Halmich 1 collaboration

Sepp Hochreiter 1 collaboration

Andreas Mayr 1 collaboration

Peter Ruch 1 collaboration

Michael Widrich 1 collaboration

Francois Berenger 1 collaboration

Ashutosh Kumar 1 collaboration

Yoshihiro Yamanishi 1 collaboration

Kam Y J Zhang 1 collaboration

Emmanuel Bengio 1 collaboration

Yoshua Bengio 1 collaboration

Moksh J Jain 1 collaboration

Maksym Korablyov 1 collaboration

Cheng-Hao Liu 1 collaboration

Gilles Marcou 1 collaboration

Enrico Glaab 1 collaboration

Kelly Barnsley 1 collaboration

Suhasini M Iyengar 1 collaboration

Mary Jo Ondrechen 1 collaboration

V Joachim Haupt 1 collaboration

Florian Kaiser 1 collaboration

Michael Schroeder 1 collaboration

Luisa Pugliese 1 collaboration

Christina Athanasiou 1 collaboration

Andrea Beccari 1 collaboration

Eleonora Gianquinto 1 collaboration

Jonas Goßen 1 collaboration

Sandra Kovachka 1 collaboration

Goutam Mukherjee 1 collaboration

Abraham Muñiz-Chicharro 1 collaboration

Giulia Paiardi 1 collaboration

S Kashif Sadiq 1 collaboration

Alexandros Tsengenes 1 collaboration

Conner Copeland 1 collaboration

Jeremiah Gaiser 1 collaboration

Daniel R Olson 1 collaboration

Amitava Roy 1 collaboration

Vishwesh Venkatraman 1 collaboration

Travis J Wheeler 1 collaboration

Haribabu Arthanari 1 collaboration

Klara Blaschitz 1 collaboration

Marco Cespugli 1 collaboration

Vedat Durmaz 1 collaboration

Konstantin Fackeldey 1 collaboration

Patrick D Fischer 1 collaboration

Christoph Gorgulla 1 collaboration

Christian Gruber 1 collaboration

Karl Gruber 1 collaboration

Michael Hetmann 1 collaboration

Jamie E Kinney 1 collaboration

Krishna M Padmanabha Das 1 collaboration

Shreya Pandita 1 collaboration

Amit Singh 1 collaboration

Georg Steinkellner 1 collaboration

Guilhem Tesseyre 1 collaboration

Gerhard Wagner 1 collaboration

Zi-Fu Wang 1 collaboration

Ryan J Yust 1 collaboration

Dmitry S Druzhilovskiy 1 collaboration

Dmitry A Filimonov 1 collaboration

Pavel V Pogodin 1 collaboration

Vladimir Poroikov 1 collaboration

Anastassia V Rudik 1 collaboration

Leonid A Stolbov 1 collaboration

Alexander V Veselovsky 1 collaboration

Maria De Rosa 1 collaboration

Giada De Simone 1 collaboration

Maria R Gulotta 1 collaboration

Jessica Lombino 1 collaboration

Nedra Mekni 1 collaboration

Ugo Perricone 1 collaboration

Arturo Casini 1 collaboration

Amanda Embree 1 collaboration

D Benjamin Gordon 1 collaboration

David Lei 1 collaboration

Katelin Pratt 1 collaboration

Christopher A Voigt 1 collaboration

Kuang-Yu Chen 1 collaboration

Yves Jacob 1 collaboration

Tim Krischuns 1 collaboration

Pierre Lafaye 1 collaboration

Agnès Zettor 1 collaboration

M Luis Rodríguez 1 collaboration

Kris M White 1 collaboration

Daren Fearon 1 collaboration

Frank Von Delft 1 collaboration

Martin A Walsh 1 collaboration

Dragos Horvath 1 collaboration

Charles L Brooks 1 collaboration

Babak Falsafi 1 collaboration

Bryan Ford 1 collaboration

Adolfo García-Sastre 1 collaboration

Sang Yup Lee 1 collaboration

Nadia Naffakh 1 collaboration

Alexandre Varnek 1 collaboration

Günter Klambauer 1 collaboration

Thomas M Hermans 1 collaboration