Parallelization of molecular docking: a review

D Dong, Z Xu, W Zhong, S Peng - Current Topics in Medicinal …, 2018 - ingentaconnect.com
Molecular docking, as one of the widely used virtual screening methods, aims to predict the
binding-conformations of small molecule ligands to the appropriate target binding site …

Detecting unknown sequences with DNA microarrays: explorative probe design strategies

E Dugat‐Bony, E Peyretaillade… - Environmental …, 2012 - Wiley Online Library
Designing environmental DNA microarrays that can be used to survey the extreme diversity
of microorganisms existing in nature, represents a stimulating challenge in the field of …

Missing genes in the annotation of prokaryotic genomes

AS Warren, J Archuleta, W Feng, JC Setubal - BMC bioinformatics, 2010 - Springer
Background Protein-coding gene detection in prokaryotic genomes is considered a much
simpler problem than in intron-containing eukaryotic genomes. However there have been …

Parallelizing BLAST and SOM algorithms with MapReduce-MPI library

SJ Sul, A Tovchigrechko - 2011 IEEE International Symposium …, 2011 - ieeexplore.ieee.org
Most bioinformatics algorithms are developed in a serial form due to a fast pace of changes
in the subject domain and the fact that many bioinformatics tasks can be parallelized as …

Coordinating computation and I/O in massively parallel sequence search

H Lin, X Ma, W Feng… - IEEE Transactions on …, 2010 - ieeexplore.ieee.org
With the explosive growth of genomic information, the searching of sequence databases has
emerged as one of the most computation and data-intensive scientific applications. Our …

Massively parallel genomic sequence search on the Blue Gene/P architecture

H Lin, P Balaji, R Poole, C Sosa, X Ma… - SC'08: Proceedings of …, 2008 - ieeexplore.ieee.org
This paper presents our first experiences in mapping and optimizing genomic sequence
search onto the massively parallel IBM Blue Gene/P (BG/P) platform. Specifically, we …

Expanding the boundaries of ligand–target modeling by exascale calculations

V Bolnykh, G Rossetti, U Rothlisberger… - Wiley Interdisciplinary …, 2021 - Wiley Online Library
Molecular simulations and molecular docking are widely used tools to investigate
ligand/target interactions and in drug design. High‐performance computing (HPC) is …

An efficient parallel implementation of the hidden markov methods for genomic sequence-search on a massively parallel system

K Jiang, O Thorsen, A Peters, B Smith… - IEEE Transactions on …, 2007 - ieeexplore.ieee.org
Bioinformatics databases used for sequence comparison and sequence alignment are
growing exponentially. This has popularized programs that carry out database searches …

Genomics as a service: A joint computing and networking perspective

G Reali, M Femminella, E Nunzi, D Valocchi - Computer Networks, 2018 - Elsevier
This paper shows a global picture of the deployment of networked processing services for
genomic data sets. Many current research and medical activities make an extensive use of …

Optimization and Performance Analysis of CAT Method for DNA Sequence Similarity Searching and Alignment

V Gancheva, H Stoev - Genes, 2024 - mdpi.com
Bioinformatics is a rapidly developing field enabling scientific experiments via computer
models and simulations. In recent years, there has been an extraordinary growth in …