The structures of all the marine and the natural products were built using Marvin Sketch (18.24, ChemAxon Ltd, Budapest, Hungary) [54 (link)]. The 2D structures were first subjected to a molecular mechanics energy minimization by the Merck molecular force field (MMFF94) present in Marvin Sketch. The protonation states the molecules were calculated assuming a neutral pH. Before the alignment for the 3D-QSAR filter and for the docking calculation, the geometry of the obtained molecular mechanics 3D structures were further optimized at semi-empirical level using the parameterized model number 3 (PM3) Hamiltonian as implemented in MOPAC package (MOPAC2016 v. 18.151, Stewart Computational Chemistry, Colorado Springs, CO, USA) [55 (link),56 (link),57 (link)].
Marvin sketch
Manufactured by Merck Group
Marvin Sketch is a software tool designed for creating and editing chemical structures and molecular diagrams. It provides a user-friendly interface for drawing, editing, and manipulating 2D representations of chemical compounds.
Automatically generated - may contain errors
Lab products found in correlation
6 protocols using marvin sketch
1
Molecular Modeling and Optimization of Natural Products
2
Molecular Structure Optimization for Docking
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The structures of all the molecules used in this study were built using Marvin Sketch (18.24, ChemAxon Ltd., Budapest, Hungary). A first molecular mechanics energy minimization was used for 3D structures created from the SMLES; the Merck molecular force field (MMFF94) present in Marvin Sketch [37 (link)] was used. The protonation states were calculated, assuming a neutral pH. The PM3 Hamiltonian, as implemented in the MOPAC package (MOPAC2016 v. 18.151, Stewart Computational Chemistry, Colorado Springs, CO, USA) [38 (link),39 (link),40 (link)], was then used to further optimize the 3D-structures before the alignment for the docking calculations.
3
Molecular Structures and Optimization
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The structures of all the molecules used in this study were built using Marvin Sketch (18.24, ChemAxon Ltd., Budapest, Hungary) [59 (link)]. A first molecular mechanics energy minimization was used for 3D structures created from the SMLES, and the Merck molecular force field (MMFF94) present in Marvin Sketch [59 (link)] was used. The protonation states were calculated assuming a neutral pH. The PM3 Hamiltonian, as implemented in the MOPAC package (MOPAC2016 v. 18.151, Stewart Computational Chemistry, Colorado Springs, CO, USA) [60 (link),61 (link),62 (link)], was then used to further optimize the 3D structures before the alignment for the 3D-QSAR filter and the docking calculations.
4
Molecular Structure Optimization via Force Field and Semi-Empirical Calculations
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The structures of the studied molecules were built using Marvin Sketch (ChemAxon, Budapest, Hungary) [58 (link)]. The 2D structures were subjected to molecular mechanics energy minimization by Merck molecular force field (MMFF94) using Marvin Sketch [58 (link)]. A pH of 7.0 was assumed for the calculation of the protonation states of the molecules. The 3D structures derived from the force field minimization were further optimized at semi-empirical level using the parameterized model number 3 (PM3) Hamiltonian using MOPAC package (Stewart Computational Chemistry, Colorado Springs, CO, USA) (vMOPAC2016) as software [59 (link),60 (link),61 (link)].
5
Ibogaine Conformational Analysis with MMFF94
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The structures of ibogaine and related compounds were built using Marvin Sketch (ChemAxon, Budapest, Hungary). The 2D structures were subjected to molecular mechanics energy minimization by Merck molecular force field (MMFF94) using the Marvin Sketch geometrical descriptors plugin. The protonation states of the molecules were calculated considering a neutral pH. Before the alignment for the 3D-QSAR filter, the geometry of the obtained 3D structures was further optimized at semi-empirical level using the parameterized model number 3 (PM3) Hamiltonian [50 (link),51 (link)] as implemented in MOPAC package (vMOPAC2016, Stewart Computational Chemistry, Colorado Springs, CO, USA) [52 ].
6
Marine Products Structure Optimization
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The structures of the marine products were built using Marvin Sketch (v. 18.24, ChemAxon Ltd., Budapest, Hungary) [64 (link)]. The 2D structures were subjected to molecular mechanics energy minimization by Merck molecular force field (MMFF94) using the Marvin Sketch geometrical descriptors plugin [64 (link)]. The protonation states of the molecules were calculated assuming a pH of 7.0. Before the alignment for the 3D-QSAR filter, the geometry of the obtained 3D structures was further optimized at the semi-empirical level using the parameterized model number 3 (PM3) Hamiltonian as implemented in the MOPAC package (MOPAC2016 v. 18.151, Stewart Computational Chemistry, Colorado Springs, CO, USA) [65 (link),66 (link),67 (link)].
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