• Memtype-2L

  • Referenced in 39 articles [sw16472]
  • interaction process with other molecules in a biological system. Particularly, with the avalanche of protein...
  • VMD

  • Referenced in 83 articles [sw18651]
  • designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid ... used to view more general molecules, as VMD can read standard Protein Data Bank...
  • Gromacs

  • Referenced in 115 articles [sw04128]
  • particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that ... also using it for research on non-biological systems, e.g. polymers...
  • PEACH

  • Referenced in 4 articles [sw10227]
  • classical and quantum simulations of biological molecules. A program package for molecular simulations of biological...
  • ABINIT-MP

  • Referenced in 3 articles [sw10528]
  • classical and quantum simulations of biological molecules. A program package for molecular simulations of biological...
  • iSuc-PseOpt

  • Referenced in 23 articles [sw22429]
  • protein molecule. Lysine succinylation plays an important role in orchestrating various biological processes...
  • PubChem

  • Referenced in 3 articles [sw23142]
  • PubChem: Integrated Platform of Small Molecules and Biological Activities. PubChem is an open repository ... experimental data identifying the biological activities of small molecules. PubChem contents include more than ... accessible platform for mining the biological information of small molecules...
  • Browndye

  • Referenced in 3 articles [sw08086]
  • diffusional encounter of two large biological molecules. It can be used to estimate second-order...
  • iCar-PseCp

  • Referenced in 18 articles [sw23951]
  • protein molecule. Carbonylation plays an important role in orchestrating various biological processes...
  • StochPy

  • Referenced in 6 articles [sw27252]
  • Tool for Simulating Stochastic Biological Processes. Single-cell and single-molecule measurements indicate the importance ... software tool for stochastic simulation in cell biology. It provides various stochastic simulation algorithms, SBML ... support, analyses of the probability distributions of molecule copy numbers and event waiting times, analyses ... gene expression, cell division, and single-molecule enzyme kinetics. StochPy has been successfully tested against...
  • Smoldyn

  • Referenced in 21 articles [sw23962]
  • over several minutes of real time. Simulated molecules diffuse, react, are confined by surfaces ... much as they would in a real biological system. Smoldyn is easy ... simulated system, support for spatial compartments, molecules with excluded volume, and simulations...
  • iROS-gPseKNC

  • Referenced in 8 articles [sw25363]
  • original DNA molecule. To in-depth understand such an important biological process...
  • pLoc_bal-mHum

  • Referenced in 9 articles [sw27662]
  • numerous protein molecules. One of the fundamental goals in molecular cell biology is to determine...
  • SDTNBI

  • Referenced in 1 article [sw23940]
  • currently millions of commercially available molecules with biologically relevant representations in chemical databases...
  • SubMAP

  • Referenced in 3 articles [sw25790]
  • number and the topology of the molecules in these alternative sets often vary from ... accurate biological alignment should be able to reveal these functionally similar molecule sets across different ... empirical results demonstrate that SubMAP can identify biologically relevant mappings that are missed by traditional...
  • ChemShell

  • Referenced in 1 article [sw21148]
  • study of small molecules, molecular crystals, biological macromolecules such as enzymes, framework materials including zeolites...
  • Frustratometer

  • Referenced in 3 articles [sw27727]
  • protein molecules. Frustration is a useful concept for gaining insights about the biological behavior ... Sites of high local frustration often indicate biologically important regions such as binding or allosteric ... constitute a stable folding core of the molecule. Thanks to its improved architecture and speed...
  • Nuc-ploc

  • Referenced in 14 articles [sw16471]
  • depth study of system biology because, in addition to helping determine their functions ... interacting with each other and with other molecules. Facing the deluge of protein sequences generated...
  • SIESTA

  • Referenced in 22 articles [sw05949]
  • initio molecular dynamics simulations of molecules and solids. SIESTA’s efficiency stems from ... being increasingly used by researchers in geosciences, biology, and engineering (apart from those...
  • iMiRNA-PseDPC

  • Referenced in 10 articles [sw22425]
  • miRNA) is a small non-coding RNA molecule, functioning in transcriptional and post-transcriptional regulation ... widely deemed as important regulators of biological processes. Aberrant expression of miRNAs has been observed...