FreeSASA: An open source C library for solvent accessible surface area calculations

Mitternacht, Simon

doi:10.12688/f1000research.7931.1

Cited by 342 publications

(287 citation statements)

References 19 publications

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“…PyMol's align function was used to perform a sequence‐guided structural alignment, and the fit of the superimposed structures was evaluated by root mean squared deviation. Solvent‐accessible surface area for http://www.rcsb.org/pdb/search/structidSearch.do?structureId=1MDT was calculated using FreeSASA .…”

Section: Methodsmentioning

confidence: 99%

Identification of a diphtheria toxin‐like gene family beyond the Corynebacterium genus

et al. 2018

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Diphtheria toxin (DT), produced by Corynebacterium diphtheria, is the causative agent of diphtheria and one of the most potent protein toxins known; however, it has an unclear evolutionary history. Here, we report the discovery of a DT-like gene family in several bacterial lineages outside of Corynebacterium, including Austwickia and Streptomyces. These DT-like genes form sister lineages in the DT phylogeny and conserve key DT features including catalytic and translocation motifs, but possess divergent receptor-binding domains. DT-like genes are not associated with corynephage, but have undergone lateral transfer through a separate mechanism. The discovery of the first non-Corynebacterium homologs of DT sheds light on its evolutionary origin and highlights novelties that may have resulted in the emergence of DT targeting humans.

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Section: Methodsmentioning

confidence: 99%

Identification of a diphtheria toxin‐like gene family beyond the Corynebacterium genus

et al. 2018

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“…For all bases for which there was modification data, true positives were considered bases with >2Å solvent accessible surface area in the crystal structure of the rabbit ribosome from 5FLX, with values transferred to homologous nucleotides for mouse. 25 …”

Section: Methodsmentioning

confidence: 99%

Interpreting Reverse Transcriptase Termination and Mutation Events for Greater Insight into the Chemical Probing of RNA

et al. 2017

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Chemical probing has the power to provide insight into RNA conformation in vivo and in vitro, but interpreting the results depends on methods to detect the chemically modified nucleotides. Traditionally, the presence of modified bases was inferred from their ability to halt reverse transcriptase during primer extension and the locations of termination sites observed by electrophoresis or sequencing. More recently, modification-induced mutations have been used as a readout for chemical probing data. Given variable propensity for mismatch incorporation and read-through with different reverse transcriptases, we examined how termination and mutation events compare to each other in the same chemical probing experiments. We found that mutations and terminations induced by dimethyl sulfate probing are both specific for methylated bases, but these two measures have surprisingly little correlation and represent largely non-overlapping indicators of chemical modification data. We also show that specific biases for modified bases depend partly on local sequence context, and that different reverse transcriptases show different biases toward reading a modification as a stop or a mutation. These results support approaches that incorporate analysis of both termination and mutation events into RNA probing experiments.

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“…We also used another package called 3V for a thorough benchmarking and found that the difference, in this case, was smaller (difference < 1%). In terms of the SA, we found that the output from the Gaussian model differs by ~6–6.5% from the vdWSA computed using the hard‐sphere model by FREESASA . Once again for a thorough benchmark, we also used NACCESS and the difference was found to be ~4.5%.…”

Section: Resultsmentioning

confidence: 97%

A grid‐based algorithm in conjunction with a gaussian‐based model of atoms for describing molecular geometry

2019

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A novel grid‐based method is presented, which in conjunction with a smooth Gaussian‐based model of atoms, is used to compute molecular volume (MV) and surface area (MSA). The MV and MSA are essential for computing nonpolar component of free energies. The objective of our grid‐based approach is to identify solute atom pairs that share overlapping volumes in space. Once completed, this information is used to construct a rooted tree using depth‐first method to yield the final volume and SA by using the formulations of the Gaussian model described by Grant and Pickup (J. Phys Chem, 1995, 99, 3503). The method is designed to function uninterruptedly with the grid‐based finite‐difference method implemented in Delphi, a popular and open‐source package used for solving the Poisson–Boltzmann equation (PBE). We demonstrate the time efficacy of the method while also validating its performance in terms of the effect of grid‐resolution, positioning of the solute within the grid‐map and accuracy in identification of overlapping atom pairs. We also explore and discuss different aspects of the Gaussian model with key emphasis on its physical meaningfulness. This development and its future release with the Delphi package are intended to provide a physically meaningful, fast, robust and comprehensive tool for MM/PBSA based free energy calculations. © 2019 Wiley Periodicals, Inc.

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FreeSASA: An open source C library for solvent accessible surface area calculations

Cited by 342 publications

References 19 publications

Identification of a diphtheria toxin‐like gene family beyond the Corynebacterium genus

Identification of a diphtheria toxin‐like gene family beyond the Corynebacterium genus

Interpreting Reverse Transcriptase Termination and Mutation Events for Greater Insight into the Chemical Probing of RNA

A grid‐based algorithm in conjunction with a gaussian‐based model of atoms for describing molecular geometry

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