Publications
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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...
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...
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...
Toward reliable density functional methods without adjustable parameters: The PBE0 model
We present an analysis of the performances of a parameter free density functional model (PBE0) obtained combining the so called PBE generalized gradient functional with a predef...
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...
The CCP4 suite: programs for protein crystallography
The CCP4 (Collaborative Computational Project, number 4) program suite is a collection of programs and associated data and subroutine libraries which can be used for macromolecu...
Cancer statistics, 2018
Abstract Each year, the American Cancer Society estimates the numbers of new cancer cases and deaths that will occur in the United States and compiles the most recent data on ca...
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i)...
A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity
Ditching Invading DNA Bacteria and archaea protect themselves from invasive foreign nucleic acids through an RNA-mediated adaptive immune system called CRISPR (clustered regular...
DETERMINATION OF SERUM PROTEINS BY MEANS OF THE BIURET REACTION
In the course of an investigation of the biochemical changes following experimental liver injury we felt the need of a simple, rapid, and accurate method for determining the pro...
Detecting Functionality-Specific Vulnerabilities via Retrieving Individual Functionality-Equivalent APIs in Open-Source Repositories
Functionality-specific vulnerabilities, which mainly occur in Application Programming Interfaces (APIs) with specific functionalities, are crucial for software developers to det...