ArticleJournal of computational chemistry2019
DelPhi Suite: New Developments and Review of Functionalities.
Article in Journal of computational chemistry, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
What it found
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Who cites it
34 citing papers in PubMed.
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- AmberTorchPB: A Unified Framework for Poisson-Boltzmann-Based Reaction Field Energy Calculation via Tensor Computation.Journal of chemical theory and computation · 2026Article
- Sources of non-Arrhenius electron transport in bacterial nanowires.Physical chemistry chemical physics : PCCP · 2026Article
- End-to-End Modeling of Reaction Field Energy Using Data-Driven Geometric Graph Neural Networks.Journal of chemical theory and computation · 2025Article
- Implicit Solvent Models and Their Applications in Biophysics.Biomolecules · 2025Review
- Prediction of aggregation in monoclonal antibodies from molecular surface curvature.Scientific reports · 2025Article
- Enzyme inhibitory activity of marine alkaloid aaptamines for neurodegenerative diseases: anRoyal Society open science · 2025Article
- Small-Molecule FICD Inhibitors Suppress Endogenous and Pathologic FICD-Mediated Protein AMPylation.ACS chemical biology · 2025Article
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- On delivering polar solvation free energy of proteins from energy minimized structures using a regularized super-Gaussian Poisson-Boltzmann model.Journal of computational chemistry · 2025Article
- Gadolinium-Based NMR Spin Relaxation Measurements of Near-Surface Electrostatic Potentials of Biomolecules.Journal of the American Chemical Society · 2024Article
- Small molecule FICD inhibitors suppress endogenous and pathologic FICD-mediated protein AMPylation.bioRxiv : the preprint server for biology · 2024Article
- Exploring the Limits of the Generalized CHARMM and AMBER Force Fields through Predictions of Hydration Free Energy of Small Molecules.Journal of chemical information and modeling · 2024Article
- Direct measurements of biomolecular electrostatics through experiments.Current opinion in structural biology · 2023Review
- Protein pJournal of chemical theory and computation · 2022Article
- Protein-Protein Binding Free Energy Predictions with the MM/PBSA Approach Complemented with the Gaussian-Based Method for Entropy Estimation.ACS omega · 2022Article
- DNA methylation cues in nucleosome geometry, stability and unwrapping.Nucleic acids research · 2022Article
- Prediction of protein pChemical science · 2022Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
Electrostatic potential, energies, and forces affect virtually any process in molecular biology, however, computing these quantities is a difficult task due to irregularly shaped macromolecules and the presence of water. Here, we report a new edition of the popular software package DelPhi along with describing its functionalities. The new DelPhi is a C++ object-oriented package supporting various levels of multiprocessing and memory distribution. It is demonstrated that multiprocessing results in significant improvement of computational time. Furthermore, for computations requiring large grid size (large macromolecular assemblages), the approach of memory distribution is shown to reduce the requirement of RAM and thus permitting large-scale modeling to be done on Linux clusters with moderate architecture. The new release comes with new features, whose functionalities and applications are described as well. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.
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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.