ArticleAngewandte Chemie (International ed. in English)2014
Multiscale modeling of biological functions: from enzymes to molecular machines (Nobel Lecture).
Article in Angewandte Chemie (International ed. in English), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
57 citing papers in PubMed.
- Article
- Fast Motions in 5 Alpha Reductase and Its Impact on Enzyme Kinetics.ACS catalysis · 2026Article
- Machine Learning-Enhanced Calculation of Quantum-Classical Binding Free Energies.Journal of chemical theory and computation · 2025Article
- Decoding Enzymatic Dechlorination with Multiscale Modeling: Mechanistic Insights into Native Haloalkane Dehalogenase fromACS catalysis · 2025Article
- Adaptive Restraints to Accelerate Geometry Optimizations of Large Biomolecular Systems.Journal of computational chemistry · 2025Article
- The Effects of Conformational Sampling and QM Region Size in QM/MM Simulations: An Adaptive QM/MM Study With Model Systems.Journal of computational chemistry · 2025Article
- Efficient Training of Neural Network Potentials for Chemical and Enzymatic Reactions by Continual Learning.Journal of chemical theory and computation · 2025Article
- A Polarizable CASSCF/MM Approach Using the Interface Between OpenMMPol Library and Cfour.Journal of computational chemistry · 2025Article
- L-DOPA Autoxidation: An Empirical Valence Bond Simulation of the Reactive Step.The journal of physical chemistry. B · 2024Article
- Targeting the conserved active site of splicing machines with specific and selective small molecule modulators.Nature communications · 2024Article
- A Vision for the Future of Multiscale Modeling.ACS physical chemistry Au · 2024Review
- Predicting Mutational Effects on CaJournal of the American Chemical Society · 2024Article
- Fine-tuning activation specificity of G-protein-coupled receptors via automated path searching.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Harnessing generative AI to decode enzyme catalysis and evolution for enhanced engineering.National science review · 2023Review
- Enhancing luciferase activity and stability through generative modeling of natural enzyme sequences.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Harnessing Generative AI to Decode Enzyme Catalysis and Evolution for Enhanced Engineering.bioRxiv : the preprint server for biology · 2023Article
- Integrated Computational Study of the Light-Activated Structure of the AppA BLUF Domain and Its Spectral Signatures.The journal of physical chemistry. A · 2023Article
- Multiscale quantum algorithms for quantum chemistry.Chemical science · 2023Article
- Induction effects on the absorption maxima of photoreceptor proteins.Biophysics and physicobiology · 2023Article
- MoBioTools: A toolkit to setup quantum mechanics/molecular mechanics calculations.Journal of computational chemistry · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
Abstract
A detailed understanding of the action of biological molecules is a pre-requisite for rational advances in health sciences and related fields. Here, the challenge is to move from available structural information to a clear understanding of the underlying function of the system. In light of the complexity of macromolecular complexes, it is essential to use computer simulations to describe how the molecular forces are related to a given function. However, using a full and reliable quantum mechanical representation of large molecular systems has been practically impossible. The solution to this (and related) problems has emerged from the realization that large systems can be spatially divided into a region where the quantum mechanical description is essential (e.g. a region where bonds are being broken), with the remainder of the system being represented on a simpler level by empirical force fields. This idea has been particularly effective in the development of the combined quantum mechanics/molecular mechanics (QM/MM) models. Here, the coupling between the electrostatic effects of the quantum and classical subsystems has been a key to the advances in describing the functions of enzymes and other biological molecules. The same idea of representing complex systems in different resolutions in both time and length scales has been found to be very useful in modeling the action of complex systems. In such cases, starting with coarse grained (CG) representations that were originally found to be very useful in simulating protein folding, and augmenting them with a focus on electrostatic energies, has led to models that are particularly effective in probing the action of molecular machines. The same multiscale idea is likely to play a major role in modeling of even more complex systems, including cells and collections of cells.
Indexed as
Identifiers
What OpenQuestion holds
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.