Related papers: ClusCo: clustering and comparison of protein model…
This paper presents a new, parallel implementation of clustering and demonstrates its utility in greatly speeding up the process of identifying homologous proteins. Clustering is a technique to reduce the number of comparison needed to find…
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…
With the upcoming generation of telescopes, cluster scale strong gravitational lenses will act as an increasingly relevant probe of cosmology and dark matter. The better resolved data produced by current and future facilities requires…
Performance of clustering algorithms is evaluated with the help of accuracy metrics. There is a great diversity of clustering algorithms, which are key components of many data analysis and exploration systems. However, there exist only few…
We present an unsupervised data processing workflow that is specifically designed to obtain a fast conformational clustering of long molecular dynamics simulation trajectories. In this approach we combine two dimensionality reduction…
Identification and alignment of three-dimensional folding of proteins may yield useful information about relationships too remote to be detected by conventional methods, such as sequence comparison, and may potentially lead to prediction of…
Modern algorithms for de novo prediction of protein structures typically output multiple full-length models (decoys) rather than a single solution. Subsequent clustering of such decoys is used both to gauge the success of the modelling and…
Clustering techniques are consolidated as a powerful strategy for analyzing the extensive data generated from molecular modeling. In particular, some tools have been developed to cluster configurations from classical simulations with a…
The genome-scale metabolic model with protein constraint (PC-model) has been increasingly popular for microbial metabolic simulations. We present PROSO Toolbox, a unified and simple-to-use PC-model toolbox that takes any high-quality…
Background and Objective: Variables collected over time, or longitudinally, such as biologic measurements in electronic health records data, are not simple to summarize with a single time-point, and thus can be more holistically…
Clustering is a popular data mining technique that aims to partition an input space into multiple homogeneous regions. There exist several clustering algorithms in the literature. The performance of a clustering algorithm depends on its…
Clustering, a fundamental activity in unsupervised learning, is notoriously difficult when the feature space is high-dimensional. Fortunately, in many realistic scenarios, only a handful of features are relevant in distinguishing clusters.…
Cluster analysis faces two problems in high dimensions: first, the `curse of dimensionality' that can lead to overfitting and poor generalization performance; and second, the sheer time taken for conventional algorithms to process large…
Similarity search is one of the most fundamental computations that are regularly performed on ever-increasing protein datasets. Scalability is of paramount importance for uncovering novel phenomena that occur at very large scales. We…
PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. While the computational cost of PLUMED…
Clustering consists of grouping together samples giving their similar properties. The problem of modeling simultaneously groups of samples and features is known as Co-Clustering. This paper introduces ROCCO - a Robust Continuous…
\texttt{rCOSA} is a software package interfaced to the R language. It implements statistical techniques for clustering objects on subsets of attributes in multivariate data. The main output of COSA is a dissimilarity matrix that one can…
As the structural databases continue to expand, efficient methods are required to search similar structures of the query structure from the database. There are many previous works about comparing protein 3D structures and scanning the…
Computational protein structure determination involves optimization in a problem space much too large to exhaustively search. Existing approaches include optimization algorithms such as gradient descent and simulated annealing, but these…
The evaluation of clustering algorithms can involve running them on a variety of benchmark problems, and comparing their outputs to the reference, ground-truth groupings provided by experts. Unfortunately, many research papers and graduate…