• GAUSSIAN

  • Referenced in 194 articles [sw06118]
  • basic laws of quantum mechanics, Gaussian predicts the energies, molecular structures, and vibrational frequencies...
  • NWChem

  • Referenced in 42 articles [sw06127]
  • computes the properties of molecular and periodic systems using quantum mechanical descriptions of the electronic ... wavefunction or density. NWChem also performs classical molecular dynamics and free energy simulations. These approaches ... perform mixed quantum-mechanics and molecular-mechanics simulations. Developed at Pacific Northwest National Laboratory, NWChem...
  • GULP

  • Referenced in 20 articles [sw01459]
  • shell model for ionic materials, molecular mechanics for organic systems, the embedded atom model...
  • VASP

  • Referenced in 16 articles [sw19550]
  • electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. VASP computes an approximate...
  • SETTLE

  • Referenced in 13 articles [sw12892]
  • algorithm in the SPASMS package of molecular mechanics and dynamics. Several series of molecular dynamics...
  • HyperChem

  • Referenced in 13 articles [sw20659]
  • animation with quantum chemical calculations, molecular mechanics, and dynamics, HyperChem puts more molecular modeling tools...
  • SMMP

  • Referenced in 12 articles [sw00882]
  • SMMP (Simple Molecular Mechanics for Proteins) package is designed for molecular simulation of linear proteins...
  • TINKER

  • Referenced in 10 articles [sw04095]
  • complete and general package for molecular mechanics and dynamics, with some special features for biopolymers ... OPLS (OPLS-UA, OPLS-AA), Merck Molecular Force Field (MMFF), Liam Dang’s polarizable model...
  • ARACNE

  • Referenced in 38 articles [sw17200]
  • elucidate functional mechanisms that underlie cellular processes and to identify molecular targets of pharmacological compounds...
  • PREMIX

  • Referenced in 52 articles [sw27815]
  • finite rate chemical kinetics and multicomponent molecular transport. After stating the appropriate governing equations ... conjunction with preprocessors for the chemical reaction mechanism and the transport properties. Transport property formulations ... using multicomponent or mixture-averaged formulas for molecular diffusion. Discussion of two example problems illustrates...
  • BALL

  • Referenced in 5 articles [sw10727]
  • structures as well as classes for Molecular Mechanics, advanced solvation methods, comparison and analysis ... have developed a stand-alone tool for molecular visualization, BALLView . BALLView makes the broad functionality...
  • Acalpred

  • Referenced in 5 articles [sw16757]
  • from its amino acid sequence in molecular mechanism clarification and the design of high efficient...
  • PLMLA

  • Referenced in 4 articles [sw36907]
  • understanding their modification dynamics and molecular mechanism. This work presents a method called PLMLA that...
  • Fu-SulfPred

  • Referenced in 3 articles [sw36890]
  • that provides critical information to understand molecular mechanisms of cell signaling transduction, stress response...
  • M.DynaMix

  • Referenced in 3 articles [sw09596]
  • most types of conventional molecular-mechanical force fields and contains a variety of auxiliary terms...
  • SPECTRUM_

  • Referenced in 2 articles [sw07647]
  • Stable numerical methods of approaching quantum mechanical molecular force fields to experimental data This paper ... molecular force fields calculation based on the joint treatment of experimental and quantum mechanical data ... nonlinear ill-posed problems. Different models of molecular force fields have been implemented...
  • UniHI

  • Referenced in 2 articles [sw17425]
  • biomedical research for the elucidation of molecular mechanisms and the identification of new modulators...
  • BOSS

  • Referenced in 2 articles [sw27537]
  • purpose molecular modeling system that performs molecular mechanics (MM) calculations, Metropolis Monte Carlo (MC) statistical...
  • iLM-2L

  • Referenced in 2 articles [sw16853]
  • functions. In order to understand the molecular mechanism of lysine methylation, it is important...
  • PVM-AMBER

  • Referenced in 1 article [sw21840]
  • parallel implementation of the AMBER molecular mechanics package for workstation clusters. A parallel version ... popular molecular mechanics package AMBER suitable for execution on workstation clusters has been developed. Computer ... intensive portions of molecular dynamics or free-energy perturbation computations, such as nonbonded pair list ... simple and cost-effective mechanism for parallel molecular dynamics simulations on readily available hardware platforms...