Related papers: FAPS: A Fast Platform for Protein Structureomics A…
Proteins are macromolecules that perform essential functions in all living organisms. Designing novel proteins with specific structures and desired functions has been a long-standing challenge in the field of bioengineering. Existing…
The integration of spatial multi-omics data from single tissues is crucial for advancing biological research. However, a significant data imbalance impedes progress: while spatial transcriptomics data is relatively abundant, spatial…
Modeling the interaction between proteins and ligands and accurately predicting their binding structures is a critical yet challenging task in drug discovery. Recent advancements in deep learning have shown promise in addressing this…
The problem of inferring proteins from complex peptide cocktails (digestion products of biological samples) in shotgun proteomic workflow sets extreme demands on computational resources in respect of the required very high processing…
Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and their amino acid sequences remains a core challenge in…
Protein retrieval, which targets the deconstruction of the relationship between sequences, structures and functions, empowers the advancing of biology. Basic Local Alignment Search Tool (BLAST), a sequence-similarity-based algorithm, has…
Mass spectrometry is the dominant technology in the field of proteomics, enabling high-throughput analysis of the protein content of complex biological samples. Due to the complexity of the instrumentation and resulting data, sophisticated…
This review article provides an overview of structurally oriented experimental datasets that can be used to benchmark protein force fields, focusing on data generated by nuclear magnetic resonance (NMR) spectroscopy and room temperature…
Several formats, including FASTA, PIR, GenBank, EMBL, and GCG, have been developed for representing protein sequences composed of natural amino acids. Among these, FASTA remains the most widely used due to its simplicity and human…
CLeFAPS, a fast and flexible pairwise structural alignment algorithm based on a rigid-body framework, namely CLePAPS, is proposed. Instead of allowing twists (or bends), the flexible in CLeFAPS means: (a) flexibilization of the algorithm's…
Protein inference plays a vital role in the proteomics study. Two major approaches could be used to handle the problem of protein inference; top-down and bottom-up. This paper presents a framework for protein inference, which uses hardware…
The idea of this project is to study the protein structure and sequence relationship using the hidden markov model and artificial neural network. In this context we have assumed two hidden markov models. In first model we have taken protein…
Understanding the relationships between protein sequence, structure and function is a long-standing biological challenge with manifold implications from drug design to our understanding of evolution. Recently, protein language models have…
Acquiring plausible pathways on high-dimensional structural distributions is beneficial in several domains. For example, in the drug discovery field, a protein conformational pathway, i.e. a highly probable sequence of protein structural…
Deep learning has contributed to major advances in the prediction of protein structure from sequence, a fundamental problem in structural bioinformatics. With predictions now approaching the accuracy of crystallographic resolution in some…
In the present work, we review the fundamental methods which have been developed in the last few years for classifying into families and clans the distribution of amino acids in protein databases. This is done through functions of random…
Membrane Proteins (MPs) account for around 15-39% of the human proteome and assume a critical role in a vast set of cellular and physiological mechanisms, including molecular transport, nutrient uptake, toxin and waste product clearance,…
Proteins are the major building blocks of life, and actuators of almost all chemical and biophysical events in living organisms. Their native structures in turn enable their biological functions which have a fundamental role in drug design.…
The comparison of computer generated protein structural models is an important element of protein structure prediction. It has many uses including model quality evaluation, selection of the final models from a large set of candidates or…
Protein phosphorylation involves the reversible modification of a protein (substrate) residue by another protein (kinase). Liquid chromatography-mass spectrometry studies are rapidly generating massive protein phosphorylation datasets…