Self-Consistent Equations Including Exchange and Correlation Effects
From a theory of Hohenberg and Kohn, approximation methods for treating an inhomogeneous system of interacting electrons are developed. These methods are exact for systems of sl...
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Fast and accurate short read alignment with Burrows–Wheeler transform
Abstract Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A...
Maximum Likelihood from Incomplete Data Via the <i>EM</i> Algorithm
Summary A broadly applicable algorithm for computing maximum likelihood estimates from incomplete data is presented at various levels of generality. Theory showing the monotone ...
Particle swarm optimization
The base isolation design usually used the historical well-known earthquake records as an input ground motion. Through the adjustment on each variables of the structure system, ...
MUSCLE: multiple sequence alignment with high accuracy and high throughput
We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting,...
CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP
The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, w...
Highly accurate protein structure prediction with AlphaFold
Abstract Proteins are essential to life, and understanding their structure can facilitate a mechanistic understanding of their function. Through an enormous experimental effort ...
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W. The new system is easy to use, providing an integrated system...
The Protein Data Bank
The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB...
Preferred Reporting Items for Systematic Reviews and Meta-Analyses: The PRISMA Statement
Systematic reviews and meta-analyses have become increasinglyimportant in health care. Clinicians readthem to keep up to date with their field (1, 2), and they areoften used as ...
KEGG: Kyoto Encyclopedia of Genes and Genomes
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional informatio...