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Image Processing
Published in Michael Ljungberg, Handbook of Nuclear Medicine and Molecular Imaging for Physicists, 2022
A classic example of a contour-based segmentation algorithm is so-called snakes [38], which is a contour that is allowed to evolve under the influence of external and internal forces. Hence, the problem of adapting the contour to the object of interest is transformed to an energy-minimization problem, with one external and one internal energy component. The external energy component makes the contour attracted to the boundary of the object of interest while the internal energy favours solutions with desirable properties, typically related to first and second derivatives of the contour, that is, the formation of discontinuities and edges are disfavoured in the minimization process. The external energy may, in principle, relate to any property of the image that is characteristic of the boundary of the object: for example the norm of the gradient of the image (i.e., a Sobel or Prewitt filtered version of the image).
Medical Image Segmentation Approach That Uses Level Sets with Statistical Shape Priors
Published in Ayman El-Baz, Jasjit S. Suri, Level Set Method in Medical Imaging Segmentation, 2019
Ahmed ElTanboly, Mohammed Ghazal, Hassan Hajjdiab, Ali Mahmoud, Ahmed Shalaby, Jasjit S. Suri, Robert Keynton, Ayman El-Baz
In this chapter, we proposed an approach for segmentation that is dependent on both the shape and the gray level intensity information. The density distribution of the input image gray values is estimated using the modified EM algorithm we introduced. This density distribution is enclosed in the PDE that governs the level set function evolution. A key step in the proposed approach, is the registration between the object to segment and the average shape, either 2–D or 3–D. In contrast to other approaches, energy minimization is not needed in our segmentation approach, which helps in staying away from the local minimum problem. We tested our approach with various image types and the results we obtained are promising. Moreover, our approach works well in segmenting noisy and inhomogeneous anatomical structures. In addition, the invariance of our approach to scaling, rotation and translation gives it significant robustness and accuracy. Accordingly, our segmentation approach can be used in various computer vision and medical imaging applications. For future work, we will investigate using our approach for 2–D and 3–D segmentation of colored objects.
Vascular Tree Segmentation from Different Image Modalities
Published in Ayman El-Baz, Jasjit S. Suri, Cardiovascular Imaging and Image Analysis, 2018
Ali Mahmoud, Ahmed Shalaby, Fatma Taher, Maryam El-Baz, Jasjit S. Suri, Ayman El-Baz
In many cases, the 3D segmentation is performed using deformable models. The mathematical foundation of such models represents the confluence of physics and geometry [10]. The latter represents an object shape and the former puts constraints on how the shape may vary over space and time. Deformable models have had great successes in imaging and computer graphics. In particular in [11], the deformable models recover the object's structure using some properties of its shape. The model evolves iteratively towards the steady state of energy minimization. But the disadvantage of this method is that the initial contour should be close to the final one. The model faces problems with topological changes of a complex structure.
Association of EFEMP1 with juvenile-onset open angle glaucoma in a patient with concomitant COL11A1-related Stickler syndrome
Published in Ophthalmic Genetics, 2023
Viney Gupta, Bindu I Somarajan, Shikha Gupta, Karthikeyan Mahalingam, Manoj Kumar, Abhishek Singh
Since EFEMP1 Arg148 is conserved among orthologues, protein structure modeling studies were performed to understand its molecular role. A three-dimensional model of human EFEMP1 was built by ITASSER using threading approach with the help of crystal structure of Notch ligand delta-like ligand 1 (Dll-1) as template (PDB: 4XBM). Both EFEMP1 and Dll-1 have epidermal growth factor, which validates the template and hence the model. The model was further refined by energy minimization and short molecular dynamics simulation to remove the template-derived constraints. Then the model of the (Arg148Cys) EFEMP1 variant was built by replacing Arg148 by Cys in native EFEMP1 model using WinCoot program followed by optimizing the conformation of Cys148 and surrounding residues. We observed that Arg148 forms hydrogen bond with Pro146 and Gln158 (Figure 3) and helps to maintain the conformation of the loop where it lies. Since EFEMP1 is known to have a role in cell adhesion and migration, loop carrying Arg148 might have important role in interactions with the cognate protein. Hence, change in loop conformation would lead to decrease in its binding to cognate proteins. The substitution of Arg148 by Cys would not be able to hold the loop in its native conformation because of its inability to form hydrogen bond with adjacent residues and having a shorter side chain compared to Arg.
Molecular docking study of britannin binding to PD-L1 and related anticancer pseudoguaianolide sesquiterpene lactones
Published in Journal of Receptors and Signal Transduction, 2022
Gérard Vergoten, Christian Bailly
The two most widely used methods to investigate protein–ligand stability and affinity are Molecular Dynamics (MD) and Monte Carlo (MC) simulations. MD simulation of proteins is a challenge which requires a careful consideration of the 1st law of thermodynamics [19]. Both methods use an empirical force field to control the total energy (MC, energy minimization) and forces (MD, Newton equations of motion). To use MD simulations confidently, a force field parameterized for dynamical properties is required. The development of a reliable and accurate force field for the conformational analysis is a concern. It requires accuracy of the force field over the whole potential surface, rather than in the region of the global minimum [20]. The most used academic force fields (CHARMM, AMBER, GROMOS) do not exhibit the required vibrational spectroscopic quality. Minimization of a protein structure with normal modes can result in the calculation of imaginary wavenumbers corresponding to maxima in the potential energy (transition states, mainly due to inadequate barriers to internal rotation). The spectroscopic SPASIBA force field has been specifically developed to provide refined empirical molecular mechanics force field parameters, as described in other studies [16,21]. For this reason, we preferred to use MC simulations rather than MD which requires a substantial increase in computer time to achieve the same level of convergence [22].
What is the current value of MM/PBSA and MM/GBSA methods in drug discovery?
Published in Expert Opinion on Drug Discovery, 2021
The MM/PB(GB)SA approach is also commonly applied for identifying new hits in virtual screening campaigns. In fact, this method should allow more robust evaluations of ligand-binding affinities than those performed by simple scoring functions employed in molecular docking algorithms. However, due to the high calculation time that characterizes this approach, the binding free energy evaluation is usually restricted to a few thousand molecules deriving from other preliminary filters and thus the MM/PB(GB)SA can be considered as a complementary strategy after previous filtering calculations. Usually, these preliminary filters consist in pharmacophore and docking evaluations, shape similarity, and in silico ADME prediction [5]. Moreover, for the same reason, very short MD simulation routines (or even just ligand-protein energy minimization protocols) are generally performed for each analyzed ligand prior to binding energy evaluation, especially in case of large datasets of ligands to be analyzed, and the entropic term is generally not considered in the calculation. In order to assess the reliability of the MM/PB(GB)SA approach for virtual screening studies, many researchers used enriched datasets containing known active molecules along with decoys and compared the predictive ability of MM/PB(GB)SA with respect to other approaches, and in particular to the scoring functions of the docking programs [4,5].