
ESPResSo
 Referenced in 17 articles
[sw06335]
 Dynamics manyparticle simulations of ”coarsegrained” beadspring models as they are used...

NFsim
 Referenced in 11 articles
[sw22256]
 advanced and flexible options for simulating coarsegrained representations of complex nonlinear reaction mechanisms ... found here. NFsim is ideal for modeling polymerization, aggregation, and cooperative reactions that cannot ... simulators. Models are specified in the BioNetGen Langauge, providing a powerful model building environment. Note ... Emonet T. Efficient modeling, simulation and coarsegraining of biological complexity with NFsim. Nature Methods...

MagiC
 Referenced in 1 article
[sw38791]
 MagiC: Software Package for Multiscale CoarseGrained Modeling. MagiC is a software package designed ... perform systematic coarsegraining of molecular models for multiscale simulations. MagiC takes input from atomistic ... GROMACS or MDynaMix), creates a coarsegrained trajectory according to a specified mapping scheme, computes ... compute effective potentials for the coarsegrained model. Such potentials can be then further used...

VOTCA
 Referenced in 1 article
[sw40481]
 Coarsegraining Applications (VOTCA) is a Coarsegrained modeling package, which focuses on the analysis ... dynamics data, the development of systematic coarsegraining techniques as well as methods used...

RNAexpNumNbors
 Referenced in 1 article
[sw23799]
 kinetics with respect to the Turner energy model for tiny (≈20 nt) RNA sequences ... binning structures into macrostates in a coarsegrained model, or by repeatedly simulating secondary structure...

PHAST
 Referenced in 1 article
[sw18806]
 single or multiple heteropolymeric chains, as coarsegrained models for proteins. The outcome data...

SELM
 Referenced in 3 articles
[sw17574]
 thermostats to extend implicitsolvent coarsegrained (ISCG) models by incorporating kinetic contributions from ... Lagrangian method (SELM). SELM couples the coarsegrained microstructure degrees of freedom to continuum stochastic ... graphical user interface (GUI) for setting up models and simulations, (iv) standardized XML formats...

REACH
 Referenced in 6 articles
[sw00788]
 program package for residuescale coarsegrained biomolecular simulation. The program calculates the force constants ... residuescale elastic network model in singledomain proteins using the variance–covariance matrix obtained ... atomistic simulation results onto a coarsegrained force field in an efficient automated procedure without...

ESPResSo++
 Referenced in 3 articles
[sw30328]
 simulation and analysis of coarsegrained atomistic or beadspring models as they are used...

MAVEN
 Referenced in 2 articles
[sw35124]
 environment that automates many of the steps. Models can be constructed from raw PDB files ... atomic coordinates or by employing various coarsegraining procedures. Visualization can be performed either with ... exported to molecular viewers. Mixed resolution models allow one to study atomic effects ... computational speed of the coarsegrained ENMs. Analysis options are available to further...

QuakeTM
 Referenced in 2 articles
[sw09534]
 task parallel model fits well. We provide a coarsegrained TM implementation characterized with eight...

downscale
 Referenced in 1 article
[sw37226]
 measure for assessing its conservation status. Coarsegrained occupancy maps are available for many taxa ... atlases, but often at spatial resolutions too coarse for conservation use. However, mapping occupancy ... area occupied increases with spatial grain size. Models that describe the OAR are fitted ... available coarsegrain sizes and then extrapolated to predict occupancy at the finer grain sizes...

HiFlow3
 Referenced in 8 articles
[sw06354]
 solution of a wide range of problems modeled by partial differential equations. Based on object ... systems – is introduced on two levels: coarsegrained parallelism by means of distributed grids...

LDEC
 Referenced in 1 article
[sw03262]
 predict the coarsegrained fracture dynamics. Two approaches to modeling these phenomena are described...

Parkway
 Referenced in 7 articles
[sw12863]
 partitioning tool. We recently proposed a coarsegrained parallel multilevel algorithm ... hypergraphs taken from the VLSI and performance modelling application domains. Further, partition quality in terms...

FlowDroid
 Referenced in 5 articles
[sw26741]
 Android use a number of coarsegrain approximations that can yield high numbers of missed ... taint analysis for Android applications. A precise model of Android’s lifecycle allows the analysis...

STMBench7
 Referenced in 9 articles
[sw08814]
 than explicit coarsegrained locking and easier to use than finegrained locking. However ... collection of operations is supported to model a wide range of workloads and concurrency patterns...

HOOMDTF
 Referenced in 2 articles
[sw40891]
 calculation; EDS Biasing (See this paper); CoarseGrained simulation force matching. In addition ... HOOMDTF makes implementing arbitrary ML models as easy as it is in TensorFlow...

DistOpt
 Referenced in 2 articles
[sw01381]
 DistOpt: A software framework for modeling and evaluating optimization problem solutions in distributed environments ... DistOpt, which is useful in building coarsegrain algorithms for solving optimization problems and simulating...

simpA
 Referenced in 7 articles
[sw00863]
 context is to devise higherlevel, coarsegrained abstractions that would help building concurrent programs ... formalizing the main aspects of this programming model...