Development and testing of a general amber force field
Abstract We describe here a general Amber force field (GAFF) for organic molecules. GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic a...
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MapReduce
MapReduce is a programming model and an associated implementation for processing and generating large datasets that is amenable to a broad variety of real-world tasks. Users spe...
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasona...
The diagnosis of dementia due to Alzheimer's disease: Recommendations from the National Institute on Aging‐Alzheimer's Association workgroups on diagnostic guidelines for Alzheimer's disease
The National Institute on Aging and the Alzheimer's Association charged a workgroup with the task of revising the 1984 criteria for Alzheimer's disease (AD) dementia. The workgr...
Hybrid functionals based on a screened Coulomb potential
Hybrid density functionals are very successful in describing a wide range of molecular properties accurately. In large molecules and solids, however, calculating the exact (Hart...
STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets
Proteins and their functional interactions form the backbone of the cellular machinery. Their connectivity network needs to be considered for the full understanding of biologica...
Efficient Estimation of Word Representations in Vector Space
We propose two novel model architectures for computing continuous vector representations of words from very large data sets. The quality of these representations is measured in ...
Numerical recipes in C: the art of scientific computing
From the Publisher: This is the revised and greatly expanded Second Edition of the hugely popular Numerical Recipes: The Art of Scientific Computing. The product of a unique co...
Birds of a Feather: Homophily in Social Networks
Similarity breeds connection. This principle—the homophily principle—structures network ties of every type, including marriage, friendship, work, advice, support, information tr...
GROMACS: Fast, flexible, and free
Abstract This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the...