CG2AT2: an Enhanced Fragment-Based Approach for Serial Multi-scale Molecular Dynamics Simulations
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Title
CG2AT2: an Enhanced Fragment-Based Approach for Serial Multi-scale Molecular Dynamics Simulations
Authors
Keywords
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Journal
Journal of Chemical Theory and Computation
Volume -, Issue -, Pages -
Publisher
American Chemical Society (ACS)
Online
2021-09-08
DOI
10.1021/acs.jctc.1c00295
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- Backmapping triangulated surfaces to coarse-grained membrane models
- (2020) Weria Pezeshkian et al. Nature Communications
- Protein–ligand binding with the coarse-grained Martini model
- (2020) Paulo C. T. Souza et al. Nature Communications
- Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS
- (2020) Szilárd Páll et al. JOURNAL OF CHEMICAL PHYSICS
- Optimization of Slipids Force Field Parameters Describing Headgroups of Phospholipids
- (2020) Fredrik Grote et al. JOURNAL OF PHYSICAL CHEMISTRY B
- UniProt: the universal protein knowledgebase in 2021
- (2020) et al. NUCLEIC ACIDS RESEARCH
- A lipid gating mechanism for the channel-forming O antigen ABC transporter
- (2019) Christopher A. Caffalette et al. Nature Communications
- Structural basis of unidirectional export of lipopolysaccharide to the cell surface
- (2019) Tristan W. Owens et al. NATURE
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- (2019) Robin A. Corey et al. Journal of Chemical Theory and Computation
- Exploring GPCR–Lipid Interactions by Molecular Dynamics Simulations: Excitements, Challenges, and the Way Forward
- (2018) Durba Sengupta et al. JOURNAL OF PHYSICAL CHEMISTRY B
- SWISS-MODEL: homology modelling of protein structures and complexes
- (2018) Andrew Waterhouse et al. NUCLEIC ACIDS RESEARCH
- Lipid–Protein Interactions Are Unique Fingerprints for Membrane Proteins
- (2018) Valentina Corradi et al. ACS Central Science
- The MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions
- (2018) Thomas D Newport et al. NUCLEIC ACIDS RESEARCH
- Structural insights into the mechanism of the membrane integral N-acyltransferase step in bacterial lipoprotein synthesis
- (2017) Maciej Wiktor et al. Nature Communications
- Coarse-Grained Protein Models and Their Applications
- (2016) Sebastian Kmiecik et al. CHEMICAL REVIEWS
- Association of Peripheral Membrane Proteins with Membranes: Free Energy of Binding of GRP1 PH Domain with Phosphatidylinositol Phosphate-Containing Model Bilayers
- (2016) Fiona B. Naughton et al. Journal of Physical Chemistry Letters
- CHARMM36m: an improved force field for folded and intrinsically disordered proteins
- (2016) Jing Huang et al. NATURE METHODS
- Crystal structure of E. coli lipoprotein diacylglyceryl transferase
- (2016) Guotao Mao et al. Nature Communications
- Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries
- (2015) Elizabeth Jefferys et al. Journal of Chemical Theory and Computation
- Structural basis for lipopolysaccharide insertion in the bacterial outer membrane
- (2014) Shuai Qiao et al. NATURE
- Molecular control of δ-opioid receptor signalling
- (2014) Gustavo Fenalti et al. NATURE
- Computational modeling of membrane proteins
- (2014) Julia Koehler Leman et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models
- (2013) Tsjerk A. Wassenaar et al. Journal of Chemical Theory and Computation
- Improved Parameters for the Martini Coarse-Grained Protein Force Field
- (2012) Djurre H. de Jong et al. Journal of Chemical Theory and Computation
- From Coarse Grained to Atomistic: A Serial Multiscale Approach to Membrane Protein Simulations
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- (2011) Scott B. Hansen et al. NATURE
- Structure and Functional Analysis of LptC, a Conserved Membrane Protein Involved in the Lipopolysaccharide Export Pathway inEscherichia coli
- (2010) An X. Tran et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation
- (2010) Maarten G. Wolf et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Reconstruction of atomistic details from coarse-grained structures
- (2010) Andrzej J. Rzepiela et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms
- (2010) Erik Wallin et al. PROTEIN SCIENCE
- Improved side-chain torsion potentials for the Amber ff99SB protein force field
- (2010) Kresten Lindorff-Larsen et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Stability of Asymmetric Lipid Bilayers Assessed by Molecular Dynamics Simulations
- (2009) Santi Esteban-Martín et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- The MARTINI Coarse-Grained Force Field: Extension to Proteins
- (2008) Luca Monticelli et al. Journal of Chemical Theory and Computation
- CHARMM-GUI: A web-based graphical user interface for CHARMM
- (2008) Sunhwan Jo et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Novel Structure of the Conserved Gram-Negative Lipopolysaccharide Transport Protein A and Mutagenesis Analysis
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