ReviewFrontiers in molecular biosciences2015
On the energy components governing molecular recognition in the framework of continuum approaches.
Review in Frontiers in molecular biosciences, 2015. 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.
- Antiviral Potential of Brown Algal Metabolites Against A179L Anti-apoptotic Protein: A Computational Strategy for African Swine Fever Treatment.Current topics in medicinal chemistry · 2026Article
- Article
- Packing and trimer-to-dimer protein reconstruction in icosahedral viral shells with a single type of symmetrical structural unit.Nanoscale advances · 2022Article
- The pH Effects on SARS-CoV and SARS-CoV-2 Spike Proteins in the Process of Binding to hACE2.Pathogens (Basel, Switzerland) · 2022Article
- The pH Effects on SARS-CoV and SARS-CoV-2 Spike Proteins in the Process of Binding to hACE2.Research square · 2021Article
- Electrostatic features for nucleocapsid proteins of SARS-CoV and SARS-CoV-2.Mathematical biosciences and engineering : MBE · 2021Article
- Hybrid method for representing ions in implicit solvation calculations.Computational and structural biotechnology journal · 2021Article
- Computational Study on DNA Repair: The Roles of Electrostatic Interactions Between Uracil-DNA Glycosylase (UDG) and DNA.Frontiers in molecular biosciences · 2021Article
- Bioactive Molecules of Tea as Potential Inhibitors for RNA-Dependent RNA Polymerase of SARS-CoV-2.Frontiers in medicine · 2021Article
- A computational model of ESAT-6 complex in membrane.Journal of theoretical & computational chemistry · 2020Article
- Spike Proteins of SARS-CoV and SARS-CoV-2 Utilize Different Mechanisms to Bind With Human ACE2.Frontiers in molecular biosciences · 2020Article
- StructureMan: A Structure Manipulation Tool to Study Large Scale Biomolecular Interactions.Frontiers in molecular biosciences · 2020Article
- A super-Gaussian Poisson-Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states.Journal of mathematical biology · 2019Article
- The Roles of Electrostatic Interactions in Capsid Assembly Mechanisms of Giant Viruses.International journal of molecular sciences · 2019Article
- Modeling Electrostatic Force in Protein-Protein Recognition.Frontiers in molecular biosciences · 2019Article
- Gaussian-Based Smooth Dielectric Function: A Surface-Free Approach for Modeling Macromolecular Binding in Solvents.Frontiers in molecular biosciences · 2018Article
- DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding.Journal of computational chemistry · 2017Article
- A New DelPhi Feature for Modeling Electrostatic Potential around Proteins: Role of Bound Ions and Implications for Zeta-Potential.Langmuir : the ACS journal of surfaces and colloids · 2017Article
- Electrostatic component of binding energy: Interpreting predictions from poisson-boltzmann equation and modeling protocols.Journal of computational chemistry · 2016Article
- Cytoplasmic dynein binding, run length, and velocity are guided by long-range electrostatic interactions.Scientific reports · 2016Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Molecular recognition is a process that brings together several biological macromolecules to form a complex and one of the most important characteristics of the process is the binding free energy. Various approaches exist to model the binding free energy, provided the knowledge of the 3D structures of bound and unbound molecules. Among them, continuum approaches are quite appealing due to their computational efficiency while at the same time providing predictions with reasonable accuracy. Here we review recent developments in the field emphasizing on the importance of adopting adequate description of physical processes taking place upon the binding. In particular, we focus on the efforts aiming at capturing some of the atomistic details of the binding phenomena into the continuum framework. When possible, the energy components are reviewed independently of each other. However, it is pointed out that rigorous approaches should consider all energy contributions on the same footage. The two major schemes for utilizing the individual energy components to predict binding affinity are outlined as well.
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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.