• APBS

  • Referenced in 95 articles [sw05766]
  • binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations to determine...
  • MIBPB

  • Referenced in 58 articles [sw08106]
  • established model for the electrostatic analysis of biomolecules. The development of advanced computational techniques ... conditions at the dielectric interface between the biomolecule and the solvent. For protein molecular surfaces ... analytically resolve the singular charge distribution in biomolecules in order to obtain reliable solutions...
  • TABI

  • Referenced in 32 articles [sw18194]
  • Poisson-Boltzmann solver for electrostatics of solvated biomolecules. We present a treecode-accelerated boundary integral ... TABI) solver for electrostatics of solvated biomolecules described by the linear Poisson-Boltzmann equation...
  • PDB2PQR

  • Referenced in 35 articles [sw13087]
  • biomolecular structures, estimating titration states and protonating biomolecules in a manner consistent with favorable hydrogen...
  • TMSmesh

  • Referenced in 21 articles [sw14719]
  • realistic mathematical modeling and numerical simulation of biomolecules, especially in implicit solvent modeling ... meshing (TMSmesh) the Gaussian surface of biomolecules. The method computes the surface points by solving...
  • Packmol

  • Referenced in 15 articles [sw13408]
  • must satisfy. Building complex mixtures, interfaces, solvating biomolecules in water, other solvents, or mixtures...
  • PBEQ-Solver

  • Referenced in 15 articles [sw17203]
  • online visualization of electrostatic potential of biomolecules. PBEQ-Solver provides a web-based graphical user...
  • Jmol

  • Referenced in 13 articles [sw15016]
  • with features for chemicals, crystals, materials and biomolecules...
  • AFMPB

  • Referenced in 12 articles [sw08875]
  • Boltzmann solver for computing the electrostatics in biomolecules. This solver combines the fast multipole method...
  • PySB

  • Referenced in 12 articles [sw13437]
  • describing interactions among multiple proteins or other biomolecules into a simple and intuitive domain specific...
  • SDPBS

  • Referenced in 7 articles [sw17208]
  • calculation of electrostatics of ionic solvated biomolecules. The Poisson-Boltzmann equation (PBE) is one important ... manipulate the molecular structure of a biomolecule, and to calculate PBE solutions in a remote...
  • FFTSVD

  • Referenced in 10 articles [sw08886]
  • Method Solver Suitable for Bio-MEMS and Biomolecule Simulation. This paper presents a fast boundary...
  • BioGRID

  • Referenced in 8 articles [sw01699]
  • interfaces for both simulations and visualization of biomolecules were developed...
  • TopologyNet

  • Referenced in 7 articles [sw41013]
  • reveal hidden structure-function relationships in biomolecules. We further integrate ESPH and convolutional neural networks...
  • ESES

  • Referenced in 4 articles [sw26786]
  • electrostatic and ion channel models. However, large biomolecules and/or fine grid resolutions give rise ... extensive tests with a large collection of biomolecule examples. Our results show that our algorithm...
  • LS-VISM

  • Referenced in 3 articles [sw16158]
  • package includes the atomic data of biomolecules under consideration and the macroscopic parameters such ... package to perform solvation analysis for biomolecules, including ligand–receptor binding systems. The package...
  • Decon2LS

  • Referenced in 3 articles [sw16610]
  • involves inferring the masses and abundances of biomolecules injected into the instrument. Because ... mass spectral patterns produced by these biomolecules, the analysis is significantly enhanced by using visualization...
  • ReaDDy

  • Referenced in 4 articles [sw17865]
  • crowding and aggregation to be modeled. The biomolecules simulated can be represented as a sphere...
  • DelPhiPKa

  • Referenced in 2 articles [sw34312]
  • calculate electrostatic potentials generated by charges of biomolecules. Topology parameters are extended to include atomic ... allows the end-user to protonate the biomolecule at particular pH based on calculated...
  • Simbody

  • Referenced in 3 articles [sw12963]
  • behavior of diverse biological mechanisms, ranging from biomolecules to human joints. Unlike their man-made...