In the past few years, 3D electron microscopy (3DEM) has undergone a revolution in instrumentation and methodology. One of the central players in this wide-reaching change is the continuous ...development of image processing software. Here we present Scipion, a software framework for integrating several 3DEM software packages through a workflow-based approach. Scipion allows the execution of reusable, standardized, traceable and reproducible image-processing protocols. These protocols incorporate tools from different programs while providing full interoperability among them. Scipion is an open-source project that can be downloaded from http://scipion.cnb.csic.es.
This Letter presents an efficient, fast, and straightforward two-step demodulating method based on a Gram-Schmidt (GS) orthonormalization approach. The phase-shift value has not to be known and can ...take any value inside the range (0,2π), excluding the singular case, where it corresponds to π. The proposed method is based on determining an orthonormalized interferogram basis from the two supplied interferograms using the GS method. We have applied the proposed method to simulated and experimental interferograms, obtaining satisfactory results. A complete MATLAB software package is provided at http://goo.gl/IZKF3.
Abstract
Motivation
Protein–Protein Interactions (PPI) are essentials for most cellular processes and thus, unveiling how proteins interact is a crucial question that can be better understood by ...identifying which residues are responsible for the interaction. Computational approaches are orders of magnitude cheaper and faster than experimental ones, leading to proliferation of multiple methods aimed to predict which residues belong to the interface of an interaction.
Results
We present BIPSPI, a new machine learning-based method for the prediction of partner-specific PPI sites. Contrary to most binding site prediction methods, the proposed approach takes into account a pair of interacting proteins rather than a single one in order to predict partner-specific binding sites. BIPSPI has been trained employing sequence-based and structural features from both protein partners of each complex compiled in the Protein–Protein Docking Benchmark version 5.0 and in an additional set independently compiled. Also, a version trained only on sequences has been developed. The performance of our approach has been assessed by a leave-one-out cross-validation over different benchmarks, outperforming state-of-the-art methods.
Availability and implementation
BIPSPI web server is freely available at http://bipspi.cnb.csic.es. BIPSPI code is available at https://github.com/bioinsilico/BIPSPI. Docker image is available at https://hub.docker.com/r/bioinsilico/bipspi/.
Supplementary information
Supplementary data are available at Bioinformatics online.
Advances in cryo-electron microscopy (cryo-EM) have made it possible to obtain structures of large biological macromolecules at near-atomic resolution. This “resolution revolution” has encouraged the ...use and development of modeling tools able to produce high-quality atomic models from cryo-EM density maps. Unfortunately, many practical problems appear when combining different packages in the same processing workflow, which make difficult the use of these tools by non-experts and, therefore, reduce their utility. We present here a major extension of the image processing framework Scipion that provides inter-package integration in the model building area and full tracking of the complete workflow, from image processing to structure validation.
We present an elastic registration algorithm for the alignment of biological images. Our method combines and extends some of the best techniques available in the context of medical imaging. We ...express the deformation field as a B-spline model, which allows us to deal with a rich variety of deformations. We solve the registration problem by minimizing a pixelwise mean-square distance measure between the target image and the warped source. The problem is further constrained by way of a vector-spline regularization which provides some control over two independent quantities that are intrinsic to the deformation: its divergence, and its curl. Our algorithm is also able to handle soft landmark constraints, which is particularly useful when parts of the images contain very little information or when its repartition is uneven. We provide an optimal analytical solution in the case when only landmarks and smoothness considerations are taken into account. We have applied our approach to perform the elastic registration of images such as electrophoretic gels and fly embryos. The validation of the results by experts has been favorable in all cases.
Cryo-EM Single Particle Analysis workflows require tens of thousands of high-quality particle projections to unveil the three-dimensional structure of macromolecules. Conventional methods for ...automatic particle picking tend to suffer from high false-positive rates, hampering the reconstruction process. One common cause of this problem is the presence of carbon and different types of high-contrast contaminations. In order to overcome this limitation, we have developed MicrographCleaner, a deep learning package designed to discriminate, in an automated fashion, between regions of micrographs which are suitable for particle picking, and those which are not. MicrographCleaner implements a U-net-like deep learning model trained on a manually curated dataset compiled from over five hundred micrographs. The benchmarking, carried out on approximately one hundred independent micrographs, shows that MicrographCleaner is a very efficient approach for micrograph preprocessing. MicrographCleaner (micrograph_cleaner_em) package is available at PyPI and Anaconda Cloud and also as a Scipion/Xmipp protocol. Source code is available at https://github.com/rsanchezgarc/micrograph_cleaner_em.
The new developments in Cryo-EM Single Particle Analysis are helping us to understand how the macromolecular structure and function meet to drive biological processes. By capturing many states at the ...particle level, it is possible to address how macromolecules explore different conformations, information that is classically extracted through 3D classification. However, the limitations of classical approaches prevent us from fully understanding the complete conformational landscape due to the reduced number of discrete states accurately reconstructed. To characterize the whole structural spectrum of a macromolecule, we propose an extension of our Zernike3D approach, able to extract per-image continuous flexibility information directly from a particle dataset. Also, our method can be seamlessly applied to images, maps or atomic models, opening integrative possibilities. Furthermore, we introduce the ZART reconstruction algorithm, which considers the Zernike3D deformation fields to revert particle conformational changes during the reconstruction process, thus minimizing the blurring induced by molecular motions.
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•Theoretically, local defocus estimation may lead to an improvement in the resolution.•A program to analyze and compare any local defocus estimation has been ...developed.•State-of-the-art methods to estimate local defocus differ considerably in their estimations.•In some cases, correction of local defocus may lead to worsening the final resolution.
Single Particle analysis (SPA) aims to determine the three-dimensional structure of proteins and macromolecular complexes. The current state of the art has allowed us to achieve near-atomic and even atomic resolutions. To obtain high-resolution structures, a set of well-defined image processing steps is required. A critical one is the estimation of the Contrast Transfer Function (CTF), which considers the sample defocus and aberrations of the microscope. Defocus is usually globally estimated; in this case, it is the same for all the particles in each micrograph. But proteins are ice-embedded at different heights, suggesting that defocus should be measured in a local (per particle) manner. There are four state-of-the-art programs to estimate local defocus (Gctf, Relion, CryoSPARC, and Xmipp). In this work, we have compared the results of these software packages to check whether the resolution improves. We have used the Scipion framework and developed a specific program to analyze local defocus. The results produced by different programs do not show a clear consensus using the current test datasets in this study.
Purpose
Biopharmaceutics examines the interrelationship of the drug’s physical/chemical properties, the dosage form (drug product) in which the drug is given, and the administration route on the rate ...and extent of sys- temic drug absorption. Pharmacokinetics is the study of the movement of drugs in the body. It uses mathematical models to evaluate the movement of absorption, distribution, metabolism, and excretion (ADME) within an organism. Finally, Pharmacodynamics is the analysis of how these drugs af- fect that organism. Pharmacokinetics data normally comes in samples over time of the drug concentration either in plasma or in some specific tissue. Similarly, pharmacodynamics data comes normally in samples over time of some quantity of interest (biophysical quantity like temperature, blood pres- sure, etc.). The data is submitted to a non-parametric analysis, in which a description of the observed data is reported (e.g., the Area Under the Curve), or to a parametric analysis by fitting a model (normally based on differential equations) so that prediction about future events can be made. This paper aims to introduce Scipion PKPD, an open-source platform for data analysis of this kind in the three domains (Biopharmaceutics, Pharmacokinetics, and Pharmacodynamics). The platform implements the most popular models and is open to new ones. The platform provides almost 100 different high-level operations that we call protocols.
Methods
We have developed a Python module integrated into the work- flow engine Scipion. The plugin implements the numerical analysis and meta- data handling tools to address multiple problems (see Suppl. Material for a detailed list of the tasks solved).
Results
We illustrate the use of this package with an integrative exam- ple that involves all these areas.
Conclusions
We show that the package successfully addresses these kinds of analyses. Scipion PKPD is freely available at
https://github.
com/cossorzano/scipion-pkpd
.
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•The field is very active in methodological exploration. The whole process aims to have better and more reproducible results from all aspects of the problem: sample preparation, image ...acquisition, image processing, and map interpretation.•The trend towards automation at all levels is essential, so that there are fewer subjective decisions, mainly in the image processing part.•Single-particle analysis is not perceived as an exhausted domain. On the contrary, it is a domain in which many additional topics are yet to be explored, as is shown by its current high publication rate.•Electron Tomography has not yet reached the explosive methodological development trend of single-particle analysis. It is undoubtedly related to the maturation of the field and the existence of still substantial issues to address.•Methodological papers are scattered in many different journals, although JSB is one of the most natural journals for them.•CryoEM as a whole has had a considerable impact in many levels of Structural, Molecular, and Cell Biology as well as in the Pharmaceutical industry.
Cryo-Electron Microscopy (CryoEM) is currently a well-established method to elucidate a biological macromolecule’s three-dimensional (3D) structure. Its success is due to technological and methodological advances in several fronts: sample preparation, electron optics and detection, image acquisition, image processing, and map interpretation. The first methods started in the late 1960s and, since then, new methods on all fronts have continuously been published, maturating the field as we know it now.
In terms of publications, we can distinguish several periods, witnessing a substantial acceleration of methodological publications in recent years, pointing out to an increased interest in the domain. On the other hand, this accelerated increase of methods development may confuse practitioners about which method they should be using (and how) and highlight the importance of paying attention to establishing best practices for methods reporting and usage.
In this paper, we analyze the trends identified in over 1,000 methodological papers. Our focus is primarily on computational image processing methods. However, our list also covers some aspects of sample preparation and image acquisition.
Several interesting ideas stem out from this study: (1) Single Particle Analysis (SPA) has largely accelerated in the last decade and sample preparation methods in the last five years; (2) Electron Tomography is not yet in a rapidly growing phase, but it is foreseeable that it will soon be; (3) the work horses of SPA are 3D classification, 3D reconstruction, and 3D alignment, and there have been many papers on these topics, which are not considered to be solved yet, but ever improving; and (4) since the resolution revolution, atomic modelling has also caught on as a hot topic.
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