ArticleProtein science : a publication of the Protein Society2004
Energy functions for protein design I: efficient and accurate continuum electrostatics and solvation.
Article in Protein science : a publication of the Protein Society, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
29 citing papers in PubMed.
- Loop engineering of AtCas9 for effective and broad genome editing.Cell insight · 2025Article
- Functionalized MoSScientific reports · 2025Article
- Yin and Yang in Post-Translational Modifications of Human D-Amino Acid Oxidase.Frontiers in molecular biosciences · 2021Article
- A physics-based energy function allows the computational redesign of a PDZ domain.Scientific reports · 2020Article
- Recent advances in automated protein design and its future challenges.Expert opinion on drug discovery · 2018Review
- Article
- Computational design of membrane proteins using RosettaMembrane.Protein science : a publication of the Protein Society · 2018Article
- Computation of pH-dependent binding free energies.Biopolymers · 2016Review
- Depth: a web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pKa of ionizable residues in proteins.Nucleic acids research · 2013Article
- Is it possible to stabilize a thermophilic protein further using sequences and structures of mesophilic proteins: a theoretical case study concerning DgAS.Theoretical biology & medical modelling · 2013Article
- Energy functions in de novo protein design: current challenges and future prospects.Annual review of biophysics · 2013Review
- Bluues: a program for the analysis of the electrostatic properties of proteins based on generalized Born radii.BMC bioinformatics · 2012Article
- Measuring the successes and deficiencies of constant pH molecular dynamics: a blind prediction study.Proteins · 2011Article
- A matching algorithm for catalytic residue site selection in computational enzyme design.Protein science : a publication of the Protein Society · 2011Article
- Article
- Computational protein design: validation and possible relevance as a tool for homology searching and fold recognition.PloS one · 2010Article
- De novo self-assembling collagen heterotrimers using explicit positive and negative design.Biochemistry · 2010Article
- Interactions between anti-ErbB2 antibody A21 and the ErbB2 extracellular domain provide a basis for improving A21 affinity.Journal of computer-aided molecular design · 2010Article
- Computer-aided design of functional protein interactions.Nature chemical biology · 2009Review
- Solvent accessible surface area approximations for rapid and accurate protein structure prediction.Journal of molecular modeling · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Electrostatics and solvation energies are important for defining protein stability, structural specificity, and molecular recognition. Because these energies are difficult to compute quickly and accurately, they are often ignored or modeled very crudely in computational protein design. To address this problem, we have developed a simple, fast, and accurate approximation for calculating Born radii in the context of protein design calculations. When these approximate Born radii are used with the generalized Born continuum dielectric model, energies calculated by the 10(6)-fold slower finite difference Poisson-Boltzmann model are faithfully reproduced. A similar approach can be used for estimating solvent-accessible surface areas (SASAs). As an independent test, we show that these approximations can be used to accurately predict the experimentally determined pK(a)s of >200 ionizable groups from 15 proteins.
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.