ArticleJournal of chemical information and modeling2022
Optimizing Multisite λ-Dynamics Throughput with Charge Renormalization.
Article in Journal of chemical information and modeling, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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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
11 citing papers in PubMed.
- Core Flipping in Lead Optimization: Rank Ordering Using λ-Dynamics.Journal of chemical information and modeling · 2025Article
- Increasing the Accuracy and Robustness of the CHARMM General Force Field with an Expanded Training Set.Journal of chemical theory and computation · 2025Article
- In silico λ-dynamics predicts protein binding specificities to modified RNAs.Nucleic acids research · 2025Article
- Superimposing Ligands with a Ligand Overlay as an Alternate Topology Model for λ-Dynamics-Based Calculations.The journal of physical chemistry. B · 2024Article
- How to Sample Dozens of Substitutions per Site with λ Dynamics.Journal of chemical theory and computation · 2024Article
- Enhanced Sampling of Buried Charges in Free Energy Calculations Using Replica Exchange with Charge Tempering.Journal of chemical theory and computation · 2024Article
- In silico λ-dynamics predicts protein binding specificities to modified RNAs.bioRxiv : the preprint server for biology · 2024Article
- Fast free energy estimates from λ-dynamics with bias-updated Gibbs sampling.Nature communications · 2023Article
- Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases.Journal of chemical information and modeling · 2023Article
- pyCHARMM: Embedding CHARMM Functionality in a Python Framework.Journal of chemical theory and computation · 2023Article
- QSAR via multisite λ-dynamics in the orphaned TSSK1B kinase.Protein science : a publication of the Protein Society · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
With the ability to sample combinations of alchemical perturbations at multiple sites off a small molecule core, multisite λ-dynamics (MSλD) has become an attractive alternative to conventional alchemical free energy methods for exploring large combinatorial chemical spaces. However, current software implementations dictate that combinatorial sampling with MSλD must be performed with a multiple topology model (MTM), which is nontrivial to create by hand, especially for a series of ligand analogues which may have diverse functional groups attached. This work introduces an automated workflow, referred to as
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.