Automatic molecular structure perception for the universal force field

Artemova, Svetlana; Jaillet, Léonard; Redon, Stéphane

doi:10.1002/jcc.24309

Cited by 28 publications

(31 citation statements)

References 45 publications

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“…To demonstrate the ability of Carbon to work with the arbitrary molecular systems and energy functions, we considered (1) a trimeric albumin protein complex (PDB ID: 5Z0B) and the GROMOS96 54a7 force field; (2) a topoisomerase complex that consists of two protein chains, one DNA fragment, two chemical compounds (PDB ID: 5GWK), and the Universal Force Field; and (3) two artificially designed nanotubes with radii of

4.0 Å

and

5.7 Å

placed one into the other using the SAMSON platform for molecular modeling, and the Brenner force field . We slightly displaced subunits from its crystallographic orientation in cases (1) and (2), thus, producing starting conformations of higher energy.…”

Section: Methodsmentioning

confidence: 99%

Controlled‐advancement rigid‐body optimization of nanosystems

et al. 2019

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In this study, we propose a novel optimization algorithm, with application to the refinement of molecular complexes. Particularly, we consider optimization problem as the calculation of quasi-static trajectories of rigid bodies influenced by the inverse-inertiaweighted energy gradient and introduce the concept of advancement region that guarantees displacement of a molecule strictly within a relevant region of conformational space. The advancement region helps to avoid typical energy minimization pitfalls, thus, the algorithm is suitable to work with arbitrary energy functions and arbitrary types of molecular complexes without necessary tuning of its hyper-parameters. Our method, called controlled-advancement rigid-body optimization of nanosystems (Carbon), is particularly useful for the large-scale molecular refinement, as for example, the putative binding candidates obtained with protein-protein docking pipelines. Implementation of Carbon with user-friendly interface is available in the SAMSON platform for molecular modeling at https://www.samson-connect.net.

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4.0 Å

and

5.7 Å

Section: Methodsmentioning

confidence: 99%

Controlled‐advancement rigid‐body optimization of nanosystems

et al. 2019

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“…Moreover, as for available perception soft-ware, it appears that only a few free tools exist [38,39,40], and they mostly focus on organic molecules. Recently, we have proposed an automatic structure perception that is well adapted for UFF [41], and on which we rely to extend UFF to IM-UFF. • A weighted atom type is an UFF atom type associated to a weight λ ∈ [0, 1].…”

Section: Continuous Molecular System Perceptionmentioning

confidence: 99%

“…the distance below which a bond between atoms i and j may be covalent, provided that considering the bond as covalent is compatible with the maximum coordination and maximum valence of atoms i and j. As in Artemova et al [41], we use:…”

Section: Definitionsmentioning

confidence: 99%

“…• co max (i) and va max (i) are the maximum coordination and maximum valence, respectively, of atom i. Their values are the same as the ones used in Artemova et al [41].…”

Section: Definitionsmentioning

confidence: 99%

“…Once weighted bonds are known, we detect covalent bonds. We use an approach very similar to the one used for UFF in Artemova et al [41]. The only difference is that, instead of relying on a cell-list approach to find covalent bonds, we search them among the weighted bonds computed at the previous step.…”

Section: Detecting Covalent Bondsmentioning

confidence: 99%

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IM-UFF: Extending the universal force field for interactive molecular modeling

Jaillet¹,

Artemova²,

Redon³

2017

Journal of Molecular Graphics and Modelling

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The universal force field (UFF) is a broadly applicable classical force field that contains parameters for almost every atom type of the periodic table. This force field is non-reactive, i.e. the topology of the system under study is considered as fixed and no creation or breaking of covalent bonds is possible. This paper introduces interactive modeling-UFF (IM-UFF), an extension of UFF that combines the possibility to significantly modify molecular structures (as with reactive force fields) with a broad diversity of supported systems thanks to the universality of UFF. Such an extension lets the user easily build and edit molecular systems interactively while being guided by physics based inter-atomic forces. This approach introduces weighted atom types and weighted bonds, used to update topologies and atom parameterizations at every time step of a simulation. IM-UFF has been evaluated on a large set of benchmarks and is proposed as a self-contained implementation integrated in a new module for the SAMSON software platform for computational nanoscience available at http://www.samson-connect.net.

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Applying Metallo‐Organic Ligand Design Principles to the Stereoselective Synthesis of a Peptide‐Based Pd₂L₄X₄ Cage

Brightwell,

Samanta,

Muldoon

et al. 2024

ChemistryEurope

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The rational and controlled synthesis of metallo‐organic cages using polyaromatic ligands is well established in the literature. There is a strong interest to advance this field towards the use of chiral ligands capable of yielding cages in a stereoselective manner. Herein, we demonstrate that the classical approach for designing metallo‐organic cages can be translated to polyproline peptides, a biocompatible class of chiral ligands. We have successfully designed a series of polyprolines, which mimic the topology of ditopic polyaromatic ligands, to achieve the stereoselective synthesis of a novel Pd lantern cage. This cage exhibits excellent stability in water and demonstrates the stabilization of a highly reactive species in solution. This work will pave the way towards the stereospecific synthesis of more complex, functionalized peptide‐based metallo‐cages.

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Automatic molecular structure perception for the universal force field

Cited by 28 publications

References 45 publications

Controlled‐advancement rigid‐body optimization of nanosystems

Controlled‐advancement rigid‐body optimization of nanosystems

IM-UFF: Extending the universal force field for interactive molecular modeling

Applying Metallo‐Organic Ligand Design Principles to the Stereoselective Synthesis of a Peptide‐Based Pd₂L₄X₄ Cage

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Automatic molecular structure perception for the universal force field

Cited by 28 publications

References 45 publications

Controlled‐advancement rigid‐body optimization of nanosystems

Controlled‐advancement rigid‐body optimization of nanosystems

IM-UFF: Extending the universal force field for interactive molecular modeling

Applying Metallo‐Organic Ligand Design Principles to the Stereoselective Synthesis of a Peptide‐Based Pd2L4X4 Cage

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Applying Metallo‐Organic Ligand Design Principles to the Stereoselective Synthesis of a Peptide‐Based Pd₂L₄X₄ Cage