Related papers: ProCaliper: functional and structural analysis, vi…

While accurate protein structure predictions are now available for nearly every observed protein sequence, predicted structures lack much of the functional context offered by experimental structure determination. We address this gap with…

The PyProcar Python package plots the band structure and the Fermi surface as a function of site and/or s,p,d,f - projected wavefunctions obtained for each $k$-point in the Brillouin zone and band in an electronic structure calculation.…

Recent advances in protein function prediction exploit graph-based deep learning approaches to correlate the structural and topological features of proteins with their molecular functions. However, proteins in vivo are not static but…

Recent advances in generative modeling show that pretrained representations can improve generation as conditioning features or alignment targets. Motivated by this, we study protein representations for predicting structures beyond…

The Protein Secondary Structure Visualizer ProS2Vi is a novel Python-based visualization tool designed to enhance the analysis and accessibility of protein secondary structures calculated and identified by the Dictionary of Secondary…

Proteins carry out biological functions through the coordinated action of groups of residues organized into structural arrangements. These arrangements, which we refer to as protein units, exist at an intermediate scale, being larger than…

Systematic identification of protein function is a key problem in current biology. Most traditional methods fail to identify functionally equivalent proteins if they lack similar sequences, structural data or extensive manual annotations.…

Protein function annotation is an important yet challenging task in biology. Recent deep learning advancements show significant potential for accurate function prediction by learning from protein sequences and structures. Nevertheless,…

Proteolysis targeting chimeras (PROTACs) are small molecules that trigger the breakdown of traditionally ``undruggable'' proteins by binding simultaneously to their targets and degradation-associated proteins. A key challenge in their…

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…

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…

Improving the ability to predict protein function can potentially facilitate research in the fields of drug discovery and precision medicine. Technically, the properties of proteins are directly or indirectly reflected in their sequence and…

Accurate identification of interactions between protein residues and ligand functional groups is essential to understand molecular recognition and guide rational drug design. Existing deep learning approaches for protein-ligand…

Protein--ligand docking is widely used in structure-based discovery, but routine studies often fail at the workflow level rather than at the scoring level. Receptor cleaning, ligand preparation, file conversion, box definition, run…

Accurately finding proteins and genes that have a certain function is the prerequisite for a broad range of biomedical applications. Despite the encouraging progress of existing computational approaches in protein function prediction, it…

Multi-modality pre-training paradigm that aligns protein sequences and biological descriptions has learned general protein representations and achieved promising performance in various downstream applications. However, these works were…

Protein function prediction is a crucial task in bioinformatics, with significant implications for understanding biological processes and disease mechanisms. While the relationship between sequence and function has been extensively…

Protein sequence analysis underpins research in biophysics, computational biology, and bioinformatics. We introduce BEER, a crossplatform graphical interface that accepts FASTA or Protein Data Bank (PDB) files, or manual sequence entry, and…

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…

One algorithm to predict protein structure is the residual dipolar coupling based residue assembly and filter tool (REDCRAFT). This algorithm exploits an exponential reduction of the search space of all possible structures to find a…