Related papers: Analysis of Three-Dimensional Protein Images
Most proteins perform their biological function by interacting with one or more molecular partners. In this respect, characterizing the features of the molecular surface, especially in the portions where the interaction takes place, turned…
Generative models trained on public databases of protein structures, most of which have been determined by X-ray crystallography, now provide powerful priors for structure prediction. However, they are not readily conditioned on the…
Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…
In this study, we present a novel approach along with the needed computational strategies for efficient and scalable feature engineering of the crystal structure in compounds of different chemical compositions. This approach utilizes a…
X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy are two powerful tools to determine the protein 3D structure. However, not all proteins can be successfully crystallized, particularly for membrane proteins. Although…
Protein structure representation is an important tool in structural biology. There exists different methods of representing the protein 3D structures and different biologists favor different methods based on the information they require.…
Cryo-Electron Microscopy (cryo-EM) has emerged as a key technology to determine the structure of proteins, particularly large protein complexes and assemblies in recent years. A key challenge in cryo-EM data analysis is to automatically…
We introduce a new model of proteins, which extends and enhances the traditional graphical representation by associating a combinatorial object called a fatgraph to any protein based upon its intrinsic geometry. Fatgraphs can easily be…
We present an efficient algorithm to recover the three dimensional structure of a protein from its contact map representation. First we show that when a physically realizable map is used as target, our method generates a structure whose…
A steadily growing computational power is employed to perform molecular dynamics simulations of biological macromolecules, which represents at the same time an immense opportunity and a formidable challenge. In fact, large amounts of data…
This paper proposes a new mathematical framework that can be applied to biological problems such as analysis of the structures of proteins and protein complexes. In particular, it gives a new method for encoding the three-dimensional…
We report a 3D structure-based method of predicting protein-protein interaction partners. It involves screening for pairs of tetrahedra representing interacting amino acids at the interface of the protein-protein complex, with one…
The mode of action of proteins is to a large extent given by their ability to adopt different conformations. This is why imaging single biomolecules at atomic resolution is one of the ultimate goals of biophysics and structural biology. The…
Due to the advancements in technology number of entries in the structural database of proteins are increasing day by day. Methods for retrieving protein tertiary structures from this large database is the key to comparative analysis of…
Cell nuclei segmentation is one of the most important tasks in the analysis of biomedical images. With ever-growing sizes and amounts of three-dimensional images to be processed, there is a need for better and faster segmentation methods.…
Semantic segmentation of raw 3D point clouds is an essential component in 3D scene analysis, but it poses several challenges, primarily due to the non-Euclidean nature of 3D point clouds. Although, several deep learning based approaches…
In this study, we tackle the challenging task of predicting secondary structures from protein primary sequences, a pivotal initial stride towards predicting tertiary structures, while yielding crucial insights into protein activity,…
Proteins constitute a large group of macromolecules with a multitude of functions for all living organisms. Proteins achieve this by adopting distinct three-dimensional structures encoded by the sequence of their constituent amino acids in…
Protein complexes are macromolecules essential to the functioning and well-being of all living organisms. As the structure of a protein complex, in particular its region of interaction between multiple protein subunits (i.e., chains), has a…
Initial protein structural comparisons were sequence-based. Since amino acids that are distant in the sequence can be close in the 3-dimensional (3D) structure, 3D contact approaches can complement sequence approaches. Traditional 3D…