• APBS

  • Referenced in 88 articles [sw05766]
  • binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations to determine...
  • MIBPB

  • Referenced in 51 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...
  • PDB2PQR

  • Referenced in 33 articles [sw13087]
  • biomolecular structures, estimating titration states and protonating biomolecules in a manner consistent with favorable hydrogen...
  • TABI

  • Referenced in 22 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...
  • TMSmesh

  • Referenced in 18 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...
  • Jmol

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

  • Referenced in 13 articles [sw17203]
  • online visualization of electrostatic potential of biomolecules. PBEQ-Solver provides a web-based graphical user...
  • Packmol

  • Referenced in 12 articles [sw13408]
  • must satisfy. Building complex mixtures, interfaces, solvating biomolecules in water, other solvents, or mixtures...
  • 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...
  • PySB

  • Referenced in 10 articles [sw13437]
  • describing interactions among multiple proteins or other biomolecules into a simple and intuitive domain specific...
  • BioGRID

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

  • Referenced in 8 articles [sw08875]
  • Boltzmann solver for computing the electrostatics in biomolecules. This solver combines the fast multipole method...
  • 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...
  • Simbody

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

  • Referenced in 3 articles [sw29361]
  • especially long noncoding RNAs (lncRNAs) and other biomolecules (proteins, mRNAs, miRNAs and genomic DNAs...
  • GIBS

  • Referenced in 1 article [sw19743]
  • Monte Carlo simulation program for simulating ion-biomolecule interactions. The ionic environment of biomolecules strongly ... solutions and their distributions around biomolecules. This software implements algorithms that automate the excess chemical...