Related papers: MEGADOCK-Web-Mito: human mitochondrial protein-pro…
Mitochondrial diseases are currently untreatable due to our limited understanding of their pathology. We study the expression of various mitochondrial proteins in skeletal myofibres (SM) in order to discover processes involved in…
Protein-protein interaction (PPI) prediction is an important problem in machine learning and computational biology. However, there is no data set for training or evaluation purposes, where all the instances are accurately labeled. Instead,…
Cold-start drug-target interaction (DTI) prediction focuses on interaction between novel drugs and proteins. Previous methods typically learn transferable interaction patterns between structures of drug and proteins to tackle it. However,…
Protein-protein interaction (PPI) extraction from published scientific literature provides additional support for precision medicine efforts. However, many of the current PPI extraction methods need extensive feature engineering and cannot…
Since the MEDLINE database was released, the number of documents indexed by this entity has risen every year. Several tools have been developed by the National Institutes of Health (NIH) to query this corpus of scientific publications.…
Protein-ligand structure prediction is an essential task in drug discovery, predicting the binding interactions between small molecules (ligands) and target proteins (receptors). Recent advances have incorporated deep learning techniques to…
Metadata-the machine-readable descriptions of the data-are increasingly seen as crucial for describing the vast array of biomedical datasets that are currently being deposited in public repositories. While most public repositories have firm…
Motivation: In recent years, protein function prediction has broken through the bottleneck of sequence features, significantly improving prediction accuracy using high-precision protein structures predicted by AlphaFold2. While…
Automatically extracting Protein-Protein Interactions (PPI) from biomedical literature provides additional support for precision medicine efforts. This paper proposes a novel memory network-based model (MNM) for PPI extraction, which…
Cellular functions are based on the complex interplay of proteins, therefore the structure and dynamics of these protein-protein interaction (PPI) networks are the key to the functional understanding of cells. In the last years, large-scale…
The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is…
Motivation: Peptides have attracted the attention in this century due to their remarkable therapeutic properties. Computational tools are being developed to take advantage of existing information, encapsulating knowledge and making it…
We propose a novel approach for predicting protein-peptide interactions using a bi-modal transformer architecture that learns an inter-facial joint distribution of residual contacts. The current data sets for crystallized protein-peptide…
Background: Alignment of biological sequences such as DNA, RNA or proteins is one of the most widely used tools in computational bioscience. All existing alignment algorithms rely on heuristic scoring schemes based on biological expertise.…
We demonstrate that Protein-Protein Interaction (PPI) networks in several eucaryotic organisms contain significantly more self-interacting proteins than expected if such homodimers randomly appeared in the course of the evolution. We also…
Reaching a global view of brain organization requires assembling evidence on widely different mental processes and mechanisms. The variety of human neuroscience concepts and terminology poses a fundamental challenge to relating brain…
Protein complexes conserved across species indicate processes that are core to cellular machinery (e.g. cell-cycle or DNA damage-repair complexes conserved across human and yeast). While numerous computational methods have been devised to…
Major histocompatibility complex class two (MHC-II) molecules are trans-membrane proteins and key components of the cellular immune system. Upon recognition of foreign peptides expressed on the MHC-II binding groove, helper T cells mount an…
Motivation: With the aim to amplify and make sense of interactions of virus-human proteins in the case of SARS-CoV-2, we performed a structural analysis of the network of protein interactions obtained from the integration of three sources:…
The protein-protein interaction (PPI) network provides an overview of the complex biological reactions vital to an organism's metabolism and survival. Even though in the past PPI network were compared across organisms in detail, there has…