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...
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2,007 publications
Scalable molecular dynamics with NAMD
Abstract NAMD is a parallel molecular dynamics code designed for high‐performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high‐end par...
Conducting Meta-Analyses in<i>R</i>with the<b>metafor</b>Package
The metafor package provides functions for conducting meta-analyses in R. The package includes functions for fitting the meta-analytic fixed- and random-effects models and allow...
The variant call format and VCFtools
Abstract Summary: The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with ...
DnaSP v5: a software for comprehensive analysis of DNA polymorphism data
Abstract Motivation: DnaSP is a software package for a comprehensive analysis of DNA polymorphism data. Version 5 implements a number of new features and analytical methods allo...
Inference from Iterative Simulation Using Multiple Sequences
The Gibbs sampler, the algorithm of Metropolis and similar iterative simulation methods are potentially very helpful for summarizing multivariate distributions. Used naively, ho...
Regularization Paths for Generalized Linear Models via Coordinate Descent
We develop fast algorithms for estimation of generalized linear models with convex penalties. The models include linear regression, two-class logistic regression, and multi- nom...
Confirmatory factor analysis for applied research
With its emphasis on practical and conceptual aspects, rather than mathematics or formulas, this accessible book has established itself as the go-to resource on confirmatory fac...
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...
Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
A new software suite, called Crystallography & NMR System (CNS), has been developed for macromolecular structure determination by X-ray crystallography or solution nuclear magne...
GENEPOP (Version 1.2): Population Genetics Software for Exact Tests and Ecumenicism
Journal Article GENEPOP (Version 1.2): Population Genetics Software for Exact Tests and Ecumenicism Get access M. Raymond, M. Raymond Institut des Sciences de l'Evolution, URA C...