CGMD Platform: Integrated Web Servers for the Preparation, Running, and Analysis of Coarse-Grained Molecular Dynamics Simulations

Molecules, vol. 25, pp. 5934

Abstract

Advances in coarse-grained molecular dynamics (CGMD) simulations have extended the use of computational studies on biological macromolecules and their complexes, as well as the interactions of membrane protein and lipid complexes at a reduced level of representation, allowing longer and larger molecular dynamics simulations. Here, we present a computational platform dedicated to the preparation, running, and analysis of CGMD simulations. The platform is built on a completely revisited version of our Martini coarsE gRained MembrAne proteIn Dynamics (MERMAID) web server, and it integrates this with other three dedicated services. In its current version, the platform expands the existing implementation of the Martini force field for membrane proteins to also allow the simulation of soluble proteins using the Martini and the SIRAH force fields. Moreover, it offers an automated protocol for carrying out the backmapping of the coarse-grained description of the system into an atomistic one.

Authors 7

1. Alessandro Marchetto Aachen Faculty of Mathematics, Computer Science and Natural Sciences

   University of Verona · Forschungszentrum Jülich · RWTH Aachen University

   Affiliation as printed

   Computational Biomedicine, Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5), Forschungszentrum Jülich, 52425 Jülich, Germany

   Department of Biotechnology, University of Verona, 37134 Verona, Italy

   Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, 52062 Aachen, Germany

2. Zeineb Si Chaib Aachen Faculty of Mathematics, Computer Science and Natural Sciences

   Forschungszentrum Jülich · RWTH Aachen University

   Affiliation as printed

   Computational Biomedicine, Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5), Forschungszentrum Jülich, 52425 Jülich, Germany

   Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, 52062 Aachen, Germany

3. Carlo Alberto Rossi

   University of Verona

   Affiliation as printed

   Department of Biotechnology, University of Verona, 37134 Verona, Italy

4. Rui Pedro Ribeiro

   University of Verona

   Affiliation as printed

   Department of Biotechnology, University of Verona, 37134 Verona, Italy

5. Sergio Pantano

   Institut Pasteur de Montevideo

   Affiliation as printed

   Institut Pasteur de Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay

6. Giulia Rossetti corresponding Aachen Department of Hematology, Oncology

   Forschungszentrum Jülich · Jülich Supercomputing Centre · RWTH Aachen University

   Affiliation as printed

   Computational Biomedicine, Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5), Forschungszentrum Jülich, 52425 Jülich, Germany

   Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, RWTH Aachen University, 52062 Aachen, Germany

   Jülich Supercomputing Center (JSC), Forschungszentrum Jülich, 52428 Jülich, Germany

7. Alejandro Giorgetti corresponding

   University of Verona · Forschungszentrum Jülich

   Affiliation as printed

   Computational Biomedicine, Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5), Forschungszentrum Jülich, 52425 Jülich, Germany

   Department of Biotechnology, University of Verona, 37134 Verona, Italy