相关论文: FSSP to SCOP and CATH (F2CS) Prediction Server
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…
Identifying interacting partners from two sets of protein sequences has important applications in computational biology. Interacting partners share similarities across species due to their common evolutionary history, and feature…
The absorption and emission of light by exoplanet atmospheres encode details of atmospheric composition, temperature, and dynamics. Fundamentally, simulating these processes requires detailed knowledge of the opacity of gases within an…
Conformal prediction is a statistical framework that generates prediction sets containing ground-truth labels with a desired coverage guarantee. The predicted probabilities produced by machine learning models are generally miscalibrated,…
The correct prediction of protein secondary structures is one of the key issues in predicting the correct protein folded shape, which is used for determining gene function. Existing methods make use of amino acids properties as indices to…
The problem of inferring proteins from complex peptide cocktails (digestion products of biological samples) in shotgun proteomic workflow sets extreme demands on computational resources in respect of the required very high processing…
We present analysis of a novel tool for protein secondary structure prediction using the recently-investigated Neural Machine Translation framework. The tool provides a fast and accurate folding prediction based on primary structure with…
Proteins are essential component of human life and their structures are important for function and mechanism analysis. Recent work has shown the potential of AI-driven methods for protein structure prediction. However, the development of…
In 2009, our group pioneered a novel method CBTOPE for predicting conformational B-cell epitopes in a protein from its amino acid sequence, which received extensive citations from the scientific community. In a recent study, Cia et al.…
The conformalClassification package implements Transductive Conformal Prediction (TCP) and Inductive Conformal Prediction (ICP) for classification problems. Conformal Prediction (CP) is a framework that complements the predictions of…
\textit{Indirect Immunofluorescence Imaging of Human Epithelial Type 2} (HEp-2) cells is an effective way to identify the presence of Anti-Nuclear Antibody (ANA). Most existing works on HEp-2 cell classification mainly focus on feature…
The comparison of computer generated protein structural models is an important element of protein structure prediction. It has many uses including model quality evaluation, selection of the final models from a large set of candidates or…
Although forward error-correction (FEC) coding is an essential part of modern fiber-optic communication systems, it is impractical to implement and evaluate FEC in transmission experiments and simulations. Therefore, it is desirable to…
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 consider the problem of calibrating an imperfect computer model using experimental data. To compensate the misspecification of the computer model and make more accurate predictions, a discrepancy function is often included and modeled…
This report presents the design of the Scope infrastructure for extensible and portable benchmarking. Improvements in high- performance computing systems rely on coordination across different levels of system abstraction. Developing and…
Scanning fluorescence correlation spectroscopy (SFCS) with a scan path perpendicular to the membrane plane was introduced to measure diffusion and interactions of fluorescent components in free standing biomembranes. Using a confocal laser…
MSstatsQC [3] is an open-source software that provides longitudinal system suitability monitoring tools in the form of control charts for proteomic experiments. It includes simultaneous tools for the mean and dispersion of suitability…
CoPreTHi is a Java based web application, which combines the results of methods that predict the location of transmembrane segments in protein sequences into a joint prediction histogram. Clearly, the joint prediction algorithm, produces…
We have focused on Answer Set Programming (ASP), more specifically, answer set counting, exploring both exact and approximate methodologies. We developed an exact ASP counter, sharpASP, which utilizes a compact encoding for propositional…