
APBS
 Referenced in 92 articles
[sw05766]
 binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations to determine...

MIBPB
 Referenced in 54 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 29 articles
[sw18194]
 PoissonBoltzmann solver for electrostatics of solvated biomolecules. We present a treecodeaccelerated boundary integral ... TABI) solver for electrostatics of solvated biomolecules described by the linear PoissonBoltzmann equation...

PDB2PQR
 Referenced in 34 articles
[sw13087]
 biomolecular structures, estimating titration states and protonating biomolecules in a manner consistent with favorable hydrogen...

TMSmesh
 Referenced in 20 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...

PBEQSolver
 Referenced in 14 articles
[sw17203]
 online visualization of electrostatic potential of biomolecules. PBEQSolver provides a webbased graphical user...

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

PySB
 Referenced in 11 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 PoissonBoltzmann equation (PBE) is one important ... manipulate the molecular structure of a biomolecule, and to calculate PBE solutions in a remote...

AFMPB
 Referenced in 10 articles
[sw08875]
 Boltzmann solver for computing the electrostatics in biomolecules. This solver combines the fast multipole method...

FFTSVD
 Referenced in 10 articles
[sw08886]
 Method Solver Suitable for BioMEMS 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 structurefunction 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...

LSVISM
 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 enduser 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 manmade...