ArticleJournal of chemical theory and computation2019
LICHEM 1.1: Recent Improvements and New Capabilities.
Article in Journal of chemical theory and computation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Comparing Force Field Treatments in QM/MM Studies of the SARS-CoV-2 RNA-Dependent RNA Polymerase (RdRp) Mechanism.Journal of chemical theory and computation · 2025Article
- Comparison of Magnesium and Manganese Ions on the Structural and Catalytic Properties of Human DNA Polymerase Gamma.Journal of chemical theory and computation · 2025Article
- Computational studies on the functional and structural impact of pathogenic mutations in enzymes.Protein science : a publication of the Protein Society · 2025Review
- Effects of the Y432S Cancer-Associated Variant on the Reaction Mechanism of Human DNA Polymerase κ.Journal of chemical information and modeling · 2024Article
- Seamless integration of GEM, a density based-force field, for QM/MM simulations via LICHEM, Psi4, and Tinker-HP.The Journal of chemical physics · 2024Article
- Relative cooperativity in neutral and charged molecular clusters using QM/MM calculations.The Journal of chemical physics · 2024Article
- Investigation of the Inhibition Mechanism of Xanthine Oxidoreductase by Oxipurinol: A Computational Study.Journal of chemical information and modeling · 2023Article
- Computational Characterization of the Inhibition Mechanism of Xanthine Oxidoreductase by Topiroxostat.ACS catalysis · 2023Article
- Distal Mutations in the β-Clamp of DNA Polymerase III* Disrupt DNA Orientation and Affect Exonuclease Activity.Journal of the American Chemical Society · 2023Article
- Computational Investigation of a Series of Small Molecules as Potential Compounds for Lysyl Hydroxylase-2 (LH2) Inhibition.Journal of chemical information and modeling · 2023Article
- Electronic Structure Effects Related to the Origin of the Remarkable Near-Infrared Absorption ofJournal of chemical theory and computation · 2022Article
- Atomistic-Level Description of the Covalent Inhibition of SARS-CoV-2 Papain-like Protease.International journal of molecular sciences · 2022Article
- Computational investigations of selected enzymes from two iron and α-ketoglutarate-dependent families.Physical chemistry chemical physics : PCCP · 2021Review
- Structural and electronic analysis of the octarepeat region of prion protein with four CuPhysical chemistry chemical physics : PCCP · 2021Article
- Combining Evolutionary Conservation and Quantum Topological Analyses To Determine Quantum Mechanics Subsystems for Biomolecular Quantum Mechanics/Molecular Mechanics Simulations.Journal of chemical theory and computation · 2021Article
- A Many-Body, Fully Polarizable Approach to QM/MM Simulations.Journal of chemical theory and computation · 2020Article
- Ewald-based methods for Gaussian integral evaluation: application to a new parameterization of GEM.Journal of molecular modeling · 2019Article
- Ground State Destabilization in Uracil DNA Glycosylase: Let's Not Forget "Tautomeric Strain" in Substrates.Journal of the American Chemical Society · 2019Article
- Towards large scale hybrid QM/MM dynamics of complex systems with advanced point dipole polarizable embeddings.Chemical science · 2019Article
- PolarizableMolecules (Basel, Switzerland) · 2018Article
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Authors and funding
3 authors.
Funding
Abstract
The QM/MM method has become a useful tool to investigate various properties of complex systems. We previously introduced the layered interacting chemical models (LICHEM) package to enable QM/MM simulations with advanced potentials by combining various (unmodified) QM and MM codes ( J. Comp. Chem., 2016, 37, 1019). LICHEM provides several capabilities such as the ability to use polarizable force fields, such as AMOEBA, for the MM environment. Here, we describe an updated version of LICHEM (v1.1), which includes several new functionalities including a new method to account for long-range electrostatic effects in QM/MM (QM/MM-LREC), a new implementation for QM/MM with the Gaussian electrostatic model (GEM), and new capabilities for path optimizations using the quadratic string model (QSM) coupled with restrained MM environment optimization.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.