ArticleJournal of chemical theory and computation2018
Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories.
Article in Journal of chemical theory and computation, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- The Role of Water in Protein-Ligand Binding: Decisive Factor, Annoying Feature, or Indispensable Control Element: In Any Case, a Major Challenge.ChemMedChem · 2026Article
- Thermodynamic Data Remain a Hot Tip for Decoding Binding Affinity and Water Impact on Protein-Ligand Complex Formation to Assist Lead Optimization.Journal of medicinal chemistry · 2026Review
- BindFlow: A Free, User-Friendly Pipeline for Absolute Binding Free Energy Calculations Using Free Energy Perturbation or MM(PB/GB)SA.Journal of chemical theory and computation · 2026Article
- Solvation Energetic Costs of Cognate Binding Site Formation.Journal of chemical information and modeling · 2025Article
- Thermodynamics of Water Displacement from Binding Sites and its Contributions to Supramolecular and Biomolecular Affinity.Angewandte Chemie (International ed. in English) · 2025Article
- Quantifying Spatially Resolved Hydration Thermodynamics Using Grid Inhomogeneous Solvation Theory [Article v1.0].Living journal of computational molecular science · 2025Article
- Ten quick tips to perform meaningful and reproducible molecular docking calculations.PLoS computational biology · 2025Article
- Engineering of Conserved Sequence Motif 1 Residues in Halohydrin Dehalogenase HheC Simultaneously Enhances Activity, Stability, and Enantioselectivity.ACS catalysis · 2025Article
- Development of Receptor Desolvation Scoring and Covalent Sampling in DOCK 6: Methods Evaluated on a RAS Test Set.Journal of chemical information and modeling · 2025Article
- Modeling Ligand Binding Site Water Networks with Site Identification by Ligand Competitive Saturation: Impact on Ligand Binding Orientations and Relative Binding Affinities.Journal of chemical theory and computation · 2024Article
- Free Energy Density of a Fluid and Its Role in Solvation and Binding.Journal of chemical theory and computation · 2024Article
- Fungi Tryptophan Synthases: What Is the Role of the Linker Connecting the α and β Structural Domains inMolecules (Basel, Switzerland) · 2024Article
- Total free energy analysis of fully hydrated proteins.Proteins · 2023Article
- Explicit solvation thermodynamics in ionic solution: extending grid inhomogeneous solvation theory to solvation free energy of salt-water mixtures.Journal of computer-aided molecular design · 2022Article
- An ATPase with a twist: A unique mechanism underlies the activity of the bacterial tyrosine kinase, Wzc.Science advances · 2021Article
- Some thermodynamic effects of varying nonpolar surfaces in protein-ligand interactions.European journal of medicinal chemistry · 2020Article
- An online repository of solvation thermodynamic and structural maps of SARS-CoV-2 targets.Journal of computer-aided molecular design · 2020Article
- Ligand design by targeting a binding site water.Chemical science · 2020Article
- Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies.Journal of chemical theory and computation · 2020Article
- An online repository of solvation thermodynamic and structural maps of SARS-CoV-2 targets.ChemRxiv : the preprint server for chemistry · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
We have developed SSTMap, a software package for mapping structural and thermodynamic water properties in molecular dynamics trajectories. The package introduces automated analysis and mapping of local measures of frustration and enhancement of water structure. The thermodynamic calculations are based on Inhomogeneous Fluid Solvation Theory (IST), which is implemented using both site-based and grid-based approaches. The package also extends the applicability of solvation analysis calculations to multiple molecular dynamics (MD) simulation programs by using existing cross-platform tools for parsing MD parameter and trajectory files. SSTMap is implemented in Python and contains both command-line tools and a Python module to facilitate flexibility in setting up calculations and for automated generation of large data sets involving analysis of multiple solutes. Output is generated in formats compatible with popular Python data science packages. This tool will be used by the molecular modeling community for computational analysis of water in problems of biophysical interest such as ligand binding and protein function.
Identifiers
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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.