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As academic interest in procedural content generation (PCG) for games has increased, so has the need for methodologies for comparing and contrasting the output spaces of alternative PCG systems. In this paper we introduce and evaluate a…
Understanding the pathways by which viral capsid proteins assemble around their genomes could identify key intermediates as potential drug targets. In this work we use computer simulations to characterize assembly over a wide range of…
Transport-Based Morphometry (TBM) has emerged as a new framework for 3D medical image analysis. By embedding images into a transport domain via invertible transformations, TBM facilitates effective classification, regression, and other…
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.…
The explosion of data throughout the biomedical sciences provides unprecedented opportunities to learn about the dynamics of evolution and disease progression, but harnessing these large and diverse datasets remains challenging. Here, we…
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics…
Enhancing cryogenic electron microscopy (cryo-EM) 3D density maps at intermediate resolution (4-8 {\AA}) is crucial in protein structure determination. Recent advances in deep learning have led to the development of automated approaches for…
Knowledge of a protein's atomic conformational ensemble is critical to determining its function, yet state-of-the-art ensemble prediction models are limited by lack of high-quality conformational data from simulation or experiment. Recent…
In understanding and redesigning the function of proteins in modern biochemistry, protein engineers are increasingly focusing on exploring regions in proteins called loops. Analyzing various characteristics of these regions helps the…
Protein-peptide interactions play a key role in cell functions. Their structural characterization, though challenging, is important for the discovery of new drugs. The CABS-dock web server provides an interface for modeling protein-peptide…
This paper introduces embComp, a novel approach for comparing two embeddings that capture the similarity between objects, such as word and document embeddings. We survey scenarios where comparing these embedding spaces is useful. From those…
Proteins encode diverse functions within complex three-dimensional structures, yet most deep learning representations remain highly entangled, obscuring the biophysical signals that underlie function. Here we introduce ProtDiS, a…
Reactions forming a pathway can be rewritten by making explicit the different molecular components involved in them. A molecular component represents a biological entity (e.g. a protein) in all its states (free, bound, degraded, etc.). In…
Dynamic graph-level embedding aims to capture structural evolution in networks, which is essential for modeling real-world scenarios. However, existing methods face two critical yet under-explored issues: Structural Visit Bias, where random…
Mapping the conformational dynamics of proteins is crucial for elucidating their functional mechanisms. While Molecular Dynamics (MD) simulation enables detailed time evolution of protein motion, its computational toll hinders its use in…
Electron cryo-microscopy (cryo-EM) produces three-dimensional (3D) maps of the electrostatic potential of biological macromolecules, including proteins. Along with knowledge about the imaged molecules, cryo-EM maps allow de novo atomic…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
The structure and function of a protein are determined by its amino acid sequence. While random mutations change a protein's sequence, evolutionary forces shape its structural fold and biological activity. Studies have shown that neutral…
Proteins move and deform to ensure their biological functions. Despite significant progress in protein structure prediction, approximating conformational ensembles at physiological conditions remains a fundamental open problem. This paper…
Graph embedding learning that aims to automatically learn low-dimensional node representations, has drawn increasing attention in recent years. To date, most recent graph embedding methods are evaluated on social and information networks…