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Proteins are large biomolecules that regulate all living organisms and consist of one or several chains. The primary structure of a protein chain is a sequence of amino acid residues whose three main atoms (alpha-carbon, nitrogen, and…
Proteins are biomolecules of life. They fold into a great variety of three-dimensional (3D) shapes. Underlying these folding patterns are many recurrent structural fragments or building blocks (analogous to `LEGO bricks'). This paper…
Protein representation learning aims to learn informative protein embeddings capable of addressing crucial biological questions, such as protein function prediction. Although sequence-based transformer models have shown promising results by…
In recent years, there has been a surge in the development of 3D structure-based pre-trained protein models, representing a significant advancement over pre-trained protein language models in various downstream tasks. However, most existing…
The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over…
Predicting protein structure from the amino acid sequence has been a challenge with theoretical and practical significance in biophysics. Despite the recent progresses elicited by improved residue-residue contact prediction, contact-based…
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 equivalent nature of 3D coordinates has posed long term challenges in protein structure representation learning, alignment, and generation. Can we create a compact and invariant language that equivalently represents protein structures?…
In this paper we show the existence of three dimensional rigid, and thus unfoldable, lattice conformations. The structure we found has 450+ bonds, and we provide a computer assisted proof of the existence of such structures. The existence…
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…
The biological function of a protein stems from its 3-dimensional structure, which is thermodynamically determined by the energetics of interatomic forces between its amino acid building blocks (the order of amino acids, known as the…
By using a mixture model for the density distribution of the three pseudobond angles formed by $C_\alpha$ atoms of four consecutive residues, the local structural states are discretized as 17 conformational letters of a protein structural…
We report a 3D structure-based method of predicting protein-protein interaction partners. It involves screening for pairs of tetrahedra representing interacting amino acids at the interface of the protein-protein complex, with one…
Protein structures are a very special class among all possible structures. It was suggested that a ``designability principle'' plays a crucial role in nature's selection of protein sequences and structures. Here we provide a theoretical…
The Automated Protein Structure Analysis (APSA) method, which describes the protein backbone as a smooth line in 3-dimensional space and characterizes it by curvature kappa and torsion tau as a function of arc length s, was applied on 77…
Structural relationships among proteins are important in the study of their evolution as well as in drug design and development. The protein 3D structure has been shown to be effective with respect to classifying proteins. Prior work has…
Learning meaningful protein representation is important for a variety of biological downstream tasks such as structure-based drug design. Having witnessed the success of protein sequence pretraining, pretraining for structural data which is…
Protein structure representation is an important tool in structural biology. There exists different methods of representing the protein 3D structures and different biologists favor different methods based on the information they require.…
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…
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…