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Jay A, Huet C, Salles N, Gunde M, Martin-Samos L, Richard N, Landa G, Goiffon V, De Gironcoli S, Hémeryck A, Mousseau N. Finding Reaction Pathways and Transition States: r-ARTn and d-ARTn as an Efficient and Versatile Alternative to String Approaches. J Chem Theory Comput 2020; 16:6726-6734. [DOI: 10.1021/acs.jctc.0c00541] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Antoine Jay
- LAAS-CNRS, Université de Toulouse, CNRS, F-31555 Toulouse, France
| | - Christophe Huet
- ISAE-SUPAERO, Université de Toulouse, F-31555 Toulouse, France
| | - Nicolas Salles
- CNR-IOM, Democritos National Simulation Center, Istituto Officina dei Materiali, c/o SISSA, via Bonomea 265, IT-34136 Trieste, Italy
| | - Miha Gunde
- LAAS-CNRS, Université de Toulouse, CNRS, F-31555 Toulouse, France
| | - Layla Martin-Samos
- CNR-IOM, Democritos National Simulation Center, Istituto Officina dei Materiali, c/o SISSA, via Bonomea 265, IT-34136 Trieste, Italy
| | | | - Georges Landa
- LAAS-CNRS, Université de Toulouse, CNRS, F-31555 Toulouse, France
| | - Vincent Goiffon
- ISAE-SUPAERO, Université de Toulouse, F-31555 Toulouse, France
| | - Stefano De Gironcoli
- CNR-IOM, Democritos National Simulation Center, Istituto Officina dei Materiali, c/o SISSA, via Bonomea 265, IT-34136 Trieste, Italy
- SISSA, via Bonomea 265, IT-34136 Trieste, Italy
| | - Anne Hémeryck
- LAAS-CNRS, Université de Toulouse, CNRS, F-31555 Toulouse, France
| | - Normand Mousseau
- Département de Physique and Regroupement québécois sur les matriaux de pointe, Département de Physique, Université de Montréal, C.P. 6128, succursale Centre-ville H3C 3J7 Montréal Canada Montréal, Canada
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Sterpone F, Melchionna S, Tuffery P, Pasquali S, Mousseau N, Cragnolini T, Chebaro Y, St-Pierre JF, Kalimeri M, Barducci A, Laurin Y, Tek A, Baaden M, Nguyen PH, Derreumaux P. The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems. Chem Soc Rev 2014; 43:4871-93. [PMID: 24759934 PMCID: PMC4426487 DOI: 10.1039/c4cs00048j] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The OPEP coarse-grained protein model has been applied to a wide range of applications since its first release 15 years ago. The model, which combines energetic and structural accuracy and chemical specificity, allows the study of single protein properties, DNA-RNA complexes, amyloid fibril formation and protein suspensions in a crowded environment. Here we first review the current state of the model and the most exciting applications using advanced conformational sampling methods. We then present the current limitations and a perspective on the ongoing developments.
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Affiliation(s)
- Fabio Sterpone
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005, Paris, France.
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Schaefer B, Mohr S, Amsler M, Goedecker S. Minima hopping guided path search: An efficient method for finding complex chemical reaction pathways. J Chem Phys 2014; 140:214102. [DOI: 10.1063/1.4878944] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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