• 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 high-throughput 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 non-uniform clusters adapted to the molecular surface. For the protein test case...
  • TINKER

  • Referenced in 10 articles [sw04095]
  • OPLS (OPLS-UA, OPLS-AA), 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...
  • PBEQ-Solver

  • 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. Car-Parrinello Molecular Dynamics (CPMD) application...
  • DeePMD-kit

  • Referenced in 2 articles [sw22318]
  • classical molecular dynamics and quantum (path-integral) 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 mixture-averaged formulas for molecular diffusion. Discussion of two example problems illustrates...
  • i-pi

  • Referenced in 1 article [sw22319]
  • Python interface for ab initio path integral molecular dynamics simulations. A Python interface ... initio path integral molecular dynamics simulations. i-PI 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 exponential-type 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...
  • GSEA-P

  • 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...
  • iLoc-Plant

  • Referenced in 18 articles [sw22419]
  • integrity. It is anticipated that iLoc-Plant 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 time-step integrators for SELM fluctuating hydrodynamics in inertial...