TY - JOUR

T1 - Web server DDfit: a new scheme to process PFG NMR diffusion data with improved precision

AU - Salikov, V.A.

AU - Lebedenko, O.O.

AU - Skrynnikov, N.R.

AU - Podkorytov, I.S.

N1 - Export Date: 09 March 2026; Cited By: 0; Correspondence Address: N.R. Skrynnikov; Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034, Russian Federation; email: n.skrynnikov@spbu.ru; I.S. Podkorytov; Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034, Russian Federation; email: i.podkorytov@spbu.ru; CODEN: JBNME

PY - 2026/2/17

Y1 - 2026/2/17

N2 - In this communication we describe a new scheme to process the data from stimulated echo protein diffusion experiments. For a series of gradient-encoded proton spectra considered over the selected spectral region, we build a model to approximate the unique (protein-dependent) shape of the spectrum. Taking a cue from the optimal filtration theory, is constructed as the intensity-weighted combination of. The so obtained is then used to fit the individual spectra, thus providing highly accurate estimates for the integral signal intensities that are subsequently used for Stejskal-Tanner-type analyses. This algorithm has been implemented as a part of a new web server, named DDfit (https://ddfit.org, mirror at https://ddfit.bio-nmr.spbu.ru/). The server accepts spectrometer data from the standard stimulated and double-stimulated echo experiments by Bruker, as well as custom-designed experiments. The server is easy to use, with data processing taking no more than several seconds. Our tests using simulated as well as experimental data found that DDfit determines protein diffusion coefficients with both accuracy and precision, offering several-fold improvement in precision compared to other processing schemes. © The Author(s), under exclusive licence to Springer Nature B.V. 2026.

AB - In this communication we describe a new scheme to process the data from stimulated echo protein diffusion experiments. For a series of gradient-encoded proton spectra considered over the selected spectral region, we build a model to approximate the unique (protein-dependent) shape of the spectrum. Taking a cue from the optimal filtration theory, is constructed as the intensity-weighted combination of. The so obtained is then used to fit the individual spectra, thus providing highly accurate estimates for the integral signal intensities that are subsequently used for Stejskal-Tanner-type analyses. This algorithm has been implemented as a part of a new web server, named DDfit (https://ddfit.org, mirror at https://ddfit.bio-nmr.spbu.ru/). The server accepts spectrometer data from the standard stimulated and double-stimulated echo experiments by Bruker, as well as custom-designed experiments. The server is easy to use, with data processing taking no more than several seconds. Our tests using simulated as well as experimental data found that DDfit determines protein diffusion coefficients with both accuracy and precision, offering several-fold improvement in precision compared to other processing schemes. © The Author(s), under exclusive licence to Springer Nature B.V. 2026.

KW - Baseline correction

KW - PFG NMR

KW - Protein diffusion

KW - Signal-to-noise optimization

KW - Spectral fitting

KW - Stimulated echo

KW - Algorithms

KW - Diffusion

KW - Internet

KW - Nuclear Magnetic Resonance, Biomolecular

KW - Proteins

KW - Software

KW - proton

KW - protein

KW - accuracy

KW - algorithm

KW - Article

KW - data processing

KW - diffusion

KW - diffusion coefficient

KW - filtration

KW - noise

KW - nuclear magnetic resonance

KW - signal processing

KW - simulation

KW - chemistry

KW - heteronuclear nuclear magnetic resonance

KW - procedures

KW - software

UR - https://www.mendeley.com/catalogue/1715cf7a-2565-39ad-b541-86440f694e76/

U2 - 10.1007/s10858-026-00487-0

DO - 10.1007/s10858-026-00487-0

M3 - статья

VL - 80

JO - Journal of Biomolecular NMR

JF - Journal of Biomolecular NMR

SN - 0925-2738

IS - 1

ER -