Related papers: PDBCirclePlot: A Novel Visualization Method for Pr…
Interactive exploration of large, multidimensional datasets plays a very important role in various scientific fields. It makes it possible not only to identify important structural features and forms, such as clusters of vertices and their…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
The similarity in the three-dimensional structures of homologous proteins imposes strong constraints on their sequence variability. It has long been suggested that the resulting correlations among amino acid compositions at different…
Several visualization schemes have been developed for imaging materials at the atomic level through atom probe tomography. The main shortcoming of these tools is their inability to parallel process data using multi-core computing units to…
We examine visual representations of data that make use of combinations of both 2D and 3D data mappings. Combining 2D and 3D representations is a common technique that allows viewers to understand multiple facets of the data with which they…
Proteins have regular tertiary structures but irregular amino acid sequences. This made it very difficult to decode the structural information in the protein sequences. Here we demonstrate that many small alpha protein domains have hidden…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Proteins are miniature machines whose function depends on their three-dimensional (3D) structure. Determining this structure computationally remains an unsolved grand challenge. A major bottleneck involves selecting the most accurate…
Protein folding is the intricate process by which a linear sequence of amino acids self-assembles into a unique three-dimensional structure. Protein folding kinetics is the study of pathways and time-dependent mechanisms a protein undergoes…
I have developed a code which allows images to be produced of a variety of interacting binaries for any system parameters. The resulting images are not only helpful in visualising the geometry of a given system but are also helpful in talks…
We present Clusterplot, a multi-class high-dimensional data visualization tool designed to visualize cluster-level information offering an intuitive understanding of the cluster inter-relations. Our unique plots leverage 2D blobs devised to…
In this and the associated article 'BioBlender: Fast and Efficient All Atom Morphing of Proteins Using Blender Game Engine', by Zini et al., we present BioBlender, a complete instrument for the elaboration of motion (Zini et al.) and the…
Perception research provides strong evidence in favor of part based representation of shapes in human visual system. Despite considerable differences among different theories in terms of how part boundaries are found, there is substantial…
Theory of multi-dimensional representation of free energy surface of protein folding is developed by adopting structural order parameters of multiple regions in protein as multiple coordinates. Various scenarios of folding are classified in…
The goal of this work is to extend the standard persistent homology pipeline for exploratory data analysis to the 2-D persistence setting, in a practical, computationally efficient way. To this end, we introduce RIVET, a software tool for…
Discovering the 3D atomic structure of molecules such as proteins and viruses is a fundamental research problem in biology and medicine. Electron Cryomicroscopy (Cryo-EM) is a promising vision-based technique for structure estimation which…
Determining the 3D structures of proteins is essential in understanding their behavior in the cellular environment. Computational methods of predicting protein structures have advanced, but assessing prediction accuracy remains a challenge.…
Motivation: Protein folding is a dynamic process during which a protein's amino acid sequence undergoes a series of 3-dimensional (3D) conformational changes en route to reaching a native 3D structure; the resulting 3D structural…
The Automated Protein Structure Analysis (APSA) method is used for the classification of supersecondary structures. Basis for the classification is the encoding of three-dimensional (3D) residue conformations into a 16-letter code (3D-1D…
Protein structure is generally conceptualized as the global arrangement or of smaller, local motifs of helices, sheets, and loops. These regular, recurring secondary structural elements have well-understood and standardized definitions in…