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Determining the structure of a protein has been a decades-long open question. A protein's three-dimensional structure often poses nontrivial computation costs, when classical simulation algorithms are utilized. Advances in the transformer…
Determining protein structures at an atomic level remains a significant challenge in structural biology. We introduce $\texttt{RecCrysFormer}$, a hybrid model that exploits the strengths of transformers with the aim of integrating…
Recent advancements in machine learning (ML) are transforming the field of structural biology. For example, AlphaFold, a groundbreaking neural network for protein structure prediction, has been widely adopted by researchers. The…
A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains…
The revolution in materials in the past century was built on a knowledge of the atomic arrangements and the structure-property relationship. The sine qua non for obtaining quantitative structural information is single crystal…
Proteins are the basic building blocks of life. They usually perform functions by folding to a particular structure. Understanding the folding process could help the researchers to understand the functions of proteins and could also help to…
Recent developments in deep learning-based methods demonstrated its potential to predict the 3D protein structures using inputs such as protein sequences, Cryo-Electron microscopy (Cryo-EM) images of proteins, etc. However, these methods…
Cryo-electron microscopy (cryo-EM) is a technique for reconstructing the 3-dimensional (3D) structure of biomolecules (especially large protein complexes and molecular assemblies). As the resolution increases to the near-atomic scale,…
The interaction of a protein with its environment can be understood and controlled via its 3D structure. Experimental methods for protein structure determination, such as X-ray crystallography or cryogenic electron microscopy, shed light on…
Predicting the structure of multi-protein complexes is a grand challenge in biochemistry, with major implications for basic science and drug discovery. Computational structure prediction methods generally leverage pre-defined structural…
Recent advancements in deep learning for predicting 3D protein structures have shown promise, particularly when leveraging inputs like protein sequences and Cryo-Electron microscopy (Cryo-EM) images. However, these techniques often fall…
The generation of protein crystals is necessary for the study of protein molecular function and structure. This is done empirically by processing large numbers of crystallization trials and inspecting them regularly in search of those with…
Proteins are essential for life, and their structure determines their function. The protein secondary structure is formed by the folding of the protein primary structure, and the protein tertiary structure is formed by the bending and…
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…
Understanding the dynamic nature of protein structures is essential for comprehending their biological functions. While significant progress has been made in predicting static folded structures, modeling protein motions on microsecond to…
Structure determination is key to understanding protein function at a molecular level. Whilst significant advances have been made in predicting structure and function from amino acid sequence, researchers must still rely on expensive,…
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…
Revealing the structure of complex biological macromolecules, such as proteins, is an essential step for understanding the chemical mechanisms that determine the diversity of their functions. Synchrotron based x-ray crystallography and…
AI-based in silico methods have improved protein structure prediction but often struggle with large protein complexes (PCs) involving multiple interacting proteins due to missing 3D spatial cues. Experimental techniques like Cryo-EM are…
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…