Related papers: bio2Byte Tools deployment as a Python package and …
The emergence of data-driven computational materials science offers unprecedented opportunities to explore complex material landscapes, complementing experimental research with the discovery of novel compounds. To enable these developments,…
The diverse nature of protein prediction tasks has traditionally necessitated specialized models, hindering the development of broadly applicable and computationally efficient Protein Language Models (PLMs). In this work, we introduce…
Delivering effective data analytics is of crucial importance to the interpretation of the multitude of biological datasets currently generated by an ever increasing number of high throughput techniques. Logic programming has much to offer…
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…
We have developed a graphical user interface (GUI) based package $\mu$2mech to perform phase-field simulation for predicting microstructure evolution. The package can take inputs from ab initio calculations and CALPHAD (Calculation of Phase…
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 analysis of experimental results with Python often requires writing many code scripts which all need access to the same set of functions. In a common field of research, this set will be nearly the same for many users. The qspec Python…
To facilitate flexible and efficient structural bioinformatics analyses, new functionality for three-dimensional structure processing and analysis has been introduced into PyCogent -- a popular feature-rich framework for sequence-based…
Machine learning has enabled differential cross section measurements that are not discretized. Going beyond the traditional histogram-based paradigm, these unbinned unfolding methods are rapidly being integrated into experimental workflows.…
Proteins are sequences of amino acids that serve as the basic building blocks of living organisms. Despite rapidly growing databases documenting structural and functional information for various protein sequences, our understanding of…
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 activity is a significant characteristic for recombinant proteins which can be used as biocatalysts. High activity of proteins reduces the cost of biocatalysts. A model that can predict protein activity from amino acid sequence is…
partycls is a Python framework for cluster analysis of systems of interacting particles. By grouping particles that share similar structural or dynamical properties, partycls enables rapid and unsupervised exploration of the system's…
Detecting microbial biomarkers used to predict disease phenotypes and clinical outcomes is crucial for disease early-stage screening and diagnosis. Most methods for biomarker identification are linear-based, which is very limited as…
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…
Despite recent advancements in deep learning methods for protein structure prediction and representation, little focus has been directed at the simultaneous inclusion and prediction of protein backbone and sidechain structure information.…
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…
PyUnfold is a Python package for incorporating imperfections of the measurement process into a data analysis pipeline. In an ideal world, we would have access to the perfect detector: an apparatus that makes no error in measuring a desired…
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…
Any cutting-edge scientific research project requires a myriad of computational tools for data generation, management, analysis and visualization. Python is a flexible and extensible scientific programming platform that offered the perfect…