ArticleJournal of chemical theory and computation2020
Predicting Reactive Cysteines with Implicit-Solvent-Based Continuous Constant pH Molecular Dynamics in Amber.
Article in Journal of chemical theory and computation, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 53 citations in OpenAlex.
- Implementation and Validation of Titratable Cysteine in GROMACS-Based Constant-pH Molecular Dynamics.Journal of chemical theory and computation · 2026Article
- Structure-based rational design of covalent probes.Communications chemistry · 2025Review
- Recent Developments in Amber Biomolecular Simulations.Journal of chemical information and modeling · 2025Article
- CIAA: Integrated Proteomics and Structural Modeling for Understanding Cysteine Reactivity with Iodoacetamide Alkyne.ACS chemical biology · 2025Article
- Exploring novel dilazep derivatives as hENT1 inhibitors and potentially covalent molecular tools.Purinergic signalling · 2025Article
- Constant pH Simulation with FMM Electrostatics in GROMACS. (A) Design and Applications.Journal of chemical theory and computation · 2025Article
- KaMLs for Predicting Protein pJournal of chemical theory and computation · 2025Article
- KaMLs for Predicting Protein pbioRxiv : the preprint server for biology · 2025Article
- Machine Learning Models to Interrogate Proteome-Wide Covalent Ligandabilities Directed at Cysteines.JACS Au · 2024Article
- phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS.Journal of chemical information and modeling · 2024Article
- Machine Learning Models to Interrogate Proteomewide Covalent Ligandabilities Directed at Cysteines.bioRxiv : the preprint server for biology · 2024Article
- PTM-Psi: A python package to facilitate the computational investigation of post-translational modification on protein structures and their impacts on dynamics and functions.Protein science : a publication of the Protein Society · 2023Article
- Quantum Descriptors for Predicting and Understanding the Structure-Activity Relationships of Michael Acceptor Warheads.Journal of chemical information and modeling · 2023Article
- Analysis of the ERK Pathway Cysteinome for Targeted Covalent Inhibition of RAF and MEK Kinases.Journal of chemical information and modeling · 2023Article
- GPU-Accelerated All-Atom Particle-Mesh Ewald Continuous Constant pH Molecular Dynamics in Amber.Journal of chemical theory and computation · 2022Article
- Cysteine Oxidation in Proteins: Structure, Biophysics, and Simulation.Biochemistry · 2022Review
- Scalable Constant pH Molecular Dynamics in GROMACS.Journal of chemical theory and computation · 2022Article
- Reactivities of the Front Pocket N-Terminal Cap Cysteines in Human Kinases.Journal of medicinal chemistry · 2022Article
- Profiling MAP kinase cysteines for targeted covalent inhibitor design.RSC medicinal chemistry · 2022Article
- A Guide to the Continuous Constant pH Molecular Dynamics Methods in Amber and CHARMM [Article v1.0].Living journal of computational molecular science · 2022Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Cysteines existing in the deprotonated thiolate form or having a tendency to become deprotonated are important players in enzymatic and cellular redox functions and frequently exploited in covalent drug design; however, most computational studies assume cysteines as protonated. Thus, developing an efficient tool that can make accurate and reliable predictions of cysteine protonation states is timely needed. We recently implemented a generalized Born (GB) based continuous constant pH molecular dynamics (CpHMD) method in Amber for protein p
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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.