Related papers: ProS2Vi: a Python Tool for Visualizing Proteins Se…
In the big data era of Astrophysics, the improvement of visualization techniques can greatly enhance the ability to identify and interpret key features in complex datasets. This aspect of data analysis will become even more relevant in the…
Proteins are fundamental biological entities that play a key role in life activities. The amino acid sequences of proteins can be folded into stable 3D structures in the real physicochemical world, forming a special kind of…
A recently introduced text classifier, called SS3, has obtained state-of-the-art performance on the CLEF's eRisk tasks. SS3 was created to deal with risk detection over text streams and, therefore, not only supports incremental training and…
Microproteins are a newly recognized and rapidly growing class of small proteins, typically encoded by fewer than 100 to 150 codons and translated from small open reading frames (smORFs). Although research has shown that smORFs and their…
PlayMolecule Viewer is a web-based data visualization toolkit designed to streamline the exploration of data resulting from structural bioinformatics or computer-aided drug design efforts. By harnessing state-of-the-art web technologies…
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…
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…
In nature the three-dimensional structure of a protein is encoded in the corresponding gene. In this paper we describe a new method for encoding the three-dimensional structure of a protein into a binary sequence. The feature of the method…
We present the VASPKIT, a command-line program that aims at providing a powerful and user-friendly interface to perform high-throughput analysis of a variety of material properties from the raw data produced by the VASP code. It consists of…
This survey for mathematicians summarizes several works by the author on protein geometry and protein function with applications to viral glycoproteins in general and the spike glycoprotein of the SARS-CoV-2 virus in particular. Background…
Software visualization helps to comprehend the system by providing a vivid illustration. The developers, as well as the analysts, can have a glance over the total system to understand the basic changes over time from a high-level point of…
We develop ProtComposer to generate protein structures conditioned on spatial protein layouts that are specified via a set of 3D ellipsoids capturing substructure shapes and semantics. At inference time, we condition on ellipsoids that are…
Background: It is necessary and essential to discovery protein function from the novel primary sequences. Wet lab experimental procedures are not only time-consuming, but also costly, so predicting protein structure and function reliably…
Protein structure tokenization converts 3D structures into discrete or vectorized representations, enabling the integration of structural and sequence data. Despite many recent works on structure tokenization, the properties of the…
Designing novel functional proteins crucially depends on accurately modeling their fitness landscape. Given the limited availability of functional annotations from wet-lab experiments, previous methods have primarily relied on…
Motivation: 3D structures of proteins provide rich information for understanding their biochemical roles. Identifying the representative protein structures for protein sequences is essential for analysis of proteins at proteome scale.…
COVID-19 has affected the world tremendously. It is critical that biological experiments and clinical designs are informed by computational approaches for time- and cost-effective solutions. Comparative analyses particularly can play a key…
The integration of artificial intelligence (AI) into pathology is advancing precision medicine by improving diagnosis, treatment planning, and patient outcomes. Digitised whole-slide images (WSIs) capture rich spatial and morphological…
Inferring the structural properties of a protein from its amino acid sequence is a challenging yet important problem in biology. Structures are not known for the vast majority of protein sequences, but structure is critical for…
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…