
KEGG
 Referenced in 265 articles
[sw13866]
 representation of the biological system, consisting of molecular building blocks of genes and proteins (genomic ... chemical information) that are integrated with the knowledge on molecular wiring diagrams of interaction, reaction...

Cytoscape
 Referenced in 76 articles
[sw09080]
 integrating biomolecular interaction networks with highthroughput expression data and other molecular states into ... framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful ... visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link...

TABI
 Referenced in 22 articles
[sw18194]
 derivative on the molecular surface. The surface is triangulated and the integral equations are discretized ... with nonuniform clusters adapted to the molecular surface. For the protein test case...

TINKER
 Referenced in 10 articles
[sw04095]
 OPLS (OPLSUA, OPLSAA), Merck Molecular Force Field (MMFF), Liam Dang’s polarizable model ... space, symplectic RESPA multiple time step integration for molecular dynamics, velocity Verlet stochastic dynamics, pairwise...

ProtoMol
 Referenced in 8 articles
[sw10728]
 rapid prototyping of novel algorithms for molecular dynamics and related applications. Its flexibility is achieved ... based on domain analysis of numerical integrators for molecular dynamics (MD) and of fast solvers...

GeneWays
 Referenced in 4 articles
[sw23128]
 system for extracting, analyzing, visualizing, and integrating molecular pathway data. The immense growth ... specialized knowledge bases for molecular biology. GeneWays is an integrated system that combines several such...

mathscape
 Referenced in 2 articles
[sw18774]
 Mathscape and molecular integrals. I have used Mathematica to solve several problems that relate ... symbolic calculation of the ‘molecular integrals’ that are a mainstay of computational chemistry. This work ... macros. Some further work on molecular integrals is presented, largely as an introduction to Mathscape...

SMILES
 Referenced in 2 articles
[sw22592]
 software. SMILES is a package for molecular integrals with Slater functions implemented by J. Fernandez ... evaluation of the different types of integrals, a summary of which can be found ... Ishida, SMILES: A package for molecular calculations with ... Recent Advances in Computational Chemistry. Molecular Integrals over Stater Orbitals, Telhat Ozdogan and Maria Belen...

PBEQSolver
 Referenced in 13 articles
[sw17203]
 tool based on MarvinSpace molecular visualization software, a Java applet integrated within CHARMM...

UNICORE
 Referenced in 17 articles
[sw02295]
 mechanisms for the integration of existing applications into UNICORE. CarParrinello Molecular Dynamics (CPMD) application...

DeePMDkit
 Referenced in 2 articles
[sw22318]
 classical molecular dynamics and quantum (pathintegral) molecular dynamics packages, i.e., LAMMPS...

PREMIX
 Referenced in 34 articles
[sw27815]
 finite rate chemical kinetics and multicomponent molecular transport. After stating the appropriate governing equations ... this algorithm is aided by invoking time integration procedures when the Newton method has convergence ... using multicomponent or mixtureaveraged formulas for molecular diffusion. Discussion of two example problems illustrates...

ipi
 Referenced in 1 article
[sw22319]
 Python interface for ab initio path integral molecular dynamics simulations. A Python interface ... initio path integral molecular dynamics simulations. iPI is composed of a Python server ... Python and Numpy) that propagates the (path integral) dynamics of the nuclei...

JRAF
 Referenced in 1 article
[sw38331]
 Molecular Auxiliary Functions. Evaluation of relativistic molecular integrals over exponentialtype spinor orbitals require using ... They are used in solution of the molecular Dirac equation for electrons moving around Coulomb ... also demonstrate how to deal with the integrals involve product of power functions with ... yielding highly accurate results for molecular integrals over a wide range of orbital parameters...

GSEAP
 Referenced in 4 articles
[sw30024]
 leading edge analysis component, seamless integration with the Molecular Signature Database (MSigDB) and an embedded...

EMBOSS
 Referenced in 35 articles
[sw10917]
 specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software ... true open source spirit. EMBOSS also integrates a range of currently available packages and tools...

iLocPlant
 Referenced in 18 articles
[sw22419]
 integrity. It is anticipated that iLocPlant may become a useful bioinformatics tool for Molecular...

PIMD
 Referenced in 1 article
[sw03372]
 shown that Fourier accelerated path integral molecular dynamics (PIMD) completely eliminates slowing down with increasing...

COVAIN
 Referenced in 1 article
[sw10556]
 reveal the systems response as an integrated molecular network. The source codes can be downloaded...

SELM
 Referenced in 3 articles
[sw17574]
 introduce a software package integrated with the molecular dynamics software LAMMPS for fluctuating hydrodynamics simulations ... SELM software include (i) numerical timestep integrators for SELM fluctuating hydrodynamics in inertial...