VMD
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Cited in
(only showing first 100 items - show all)- PROSIGN: a method for protein secondary structure assignment based on three-dimensional coordinates of consecutive \(C_\alpha \) atoms
- Large deformation and fracture mechanics of a beta-helical protein nanotube: Atomistic and continuum modeling
- Analyses of tensile deformation of nanocrystalline \(\alpha-\text{Fe}_2\text{O}_3+fcc-\)Al composites using molecular dynamics simulations
- Modelling excess surface energy in dry and wetted calcite systems
- Algorithmic challenges in computational molecular biophysics
- NAMD2: Greater scalability for parallel molecular dynamics
- Qprop
- AMBER
- GAMESS
- NAMD
- Large-scale molecular dynamics simulation of flow under complex structure of endothelial glycocalyx
- TINKER
- Gromacs
- SimMechanics
- SDPhound, a mutual information-based method to investigate specificity-determining positions
- A fast mollified impulse method for biomolecular atomistic simulations
- Understanding the intracellular-to-extracellular localization switch of polyhydroxybutyrate polymerase in \textit{Pseudomonas} backgrounds as a microevolutionary process
- Insights into the molecular mechanisms of protein-ligand interactions by molecular docking and molecular dynamics simulation: a case of oligopeptide binding protein
- A novel canonical dual computational approach for prion AGAAAAGA amyloid fibril molecular modeling
- APBS
- Analyzing the sequence-structure relationship of a library of local structural prototypes
- LAMMPS
- CHARMM
- PLUMED
- DMOL3
- ESPResSo
- AdResS
- PetFMM
- Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUs and a billion unknowns
- PNFFT
- Myoglobin ligand gate mechanism analysis by a novel 3D visualization technique
- Using sacrificial cell spheroids for the bioprinting of perfusable 3D tissue and organ constructs: a computational study
- Browndye
- Macrodox
- SDA
- GROMOS
- Evolutionary de Rham-Hodge method
- DYANA
- Viral capsid nanoindentation simulations using octree-type data structures
- LINCS
- FFTSVD
- Fastcap
- DL_POLY
- DL_POLY_3
- Topological data analysis for the energy and stability of endohedral metallofullerenes
- Periodic boundary conditions for arbitrary deformations in molecular dynamics simulations
- Dynamic pull-in instability of multilayer graphene NEMSs: non-classical continuum model and molecular dynamics simulations
- Molecular advection-diffusion through graphene nanopores
- M.DynaMix
- NAMD2
- AutoDock Vina
- PyMOL
- Using computational approaches to study dengue virus capsid assembly
- CIF2Cell
- edgecount
- Chimera
- Ribosome Builder
- A comparative molecular dynamics-phase-field modeling approach to brittle fracture
- Revisiting chameleon sequences in the protein data bank
- TK
- Computational study of thermal dependence of accommodation coefficients in a nano-channel and the prediction of velocity profiles
- Mechanics of water pore formation in lipid membrane under electric field
- The fuzzy oil drop model, based on hydrophobicity density distribution, generalizes the influence of water environment on protein structure and function
- Minimizing the object dimensions in circle and sphere packing problems
- SETTLE
- Ribosome Builder: a software project to simulate the ribosome
- Visualizing the dual space of biological molecules
- PDB2PQR
- X-PLOR
- Geometry-guided computation of 3D electrostatics for large biomolecules
- SYBYL
- Efficient perturbation analysis of elastic network models -- application to acetylcholinesterase of T. Californica
- OVITO
- Jmol
- Avogadro
- 2Dhp90
- Structural and energetic comparison of the complexes of aminoglycosides with the model of the ribosomal A-site
- Petri nets formalism facilitates analysis of complex biomolecular structural data
- VARNA
- MINT
- DeepVS
- ESPResSo 3.1: Molecular Dynamics Software for Coarse-Grained Models
- Statistical mechanical theory of protein folding in water environment
- PAFMPB
- The solution of the boundary-value problems for the simulation of transition of protein confor\-mation
- PBEQ-Solver
- I-TASSER
- SDPBS
- DelPhi Web Server
- QMEAN
- TABI
- MUI
- Accuracy limits of the blob model for a flexible polymer confined inside a cylindrical nano-channel
- MMM2D
- Voreen
- VENLO
- BioSG
- FPV
- RasMol
- WEAVE
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