NanoCrystal: A Web-Based Crystallographic Tool for the Construction of Nanoparticles Based on Their Crystal Habit

Modeling of nanoparticles is an essential first step to assess their capacities for different uses such as energy storage and drug delivery. However, creating an initial starting conformation for modeling and simulation is tedious because every crystalline material grows with a different crystal habit. In this application note, we describe NanoCrystal, a novel web-based crystallographic tool that creates nanoparticle models from any crystal structure guided by their preferred equilibrium shape under standard conditions according to the Wulff morphology (crystal habit). Users can upload a cif file, define the Miller indices and their corresponding minimum surface energies according to the Wulff construction of a particular crystal, and specify the size of the nanocrystal. As a result, the nanoparticle is constructed and visualized, and the coordinates of the atoms are output to the user. NanoCrystal can be accessed at http://nanocrystal.vi-seem.edu/

NanoCrystal: A Web-Based Crystallographic Tool for the Construction of Nanoparticles Based on Their Crystal Habit

Modeling of nanoparticles is an essential first step to assess their capacities for different uses such as energy storage and drug delivery. However, creating an initial starting conformation for modeling and simulation is tedious because every crystalline material grows with a different crystal habit. In this application note, we describe NanoCrystal, a novel web-based crystallographic tool that creates nanoparticle models from any crystal structure guided by their preferred equilibrium shape under standard conditions according to the Wulff morphology (crystal habit). Users can upload a cif file, define the Miller indices and their corresponding minimum surface energies according to the Wulff construction of a particular crystal, and specify the size of the nanocrystal. As a result, the nanoparticle is constructed and visualized, and the coordinates of the atoms are output to the user. NanoCrystal can be accessed at http://nanocrystal.vi-seem.edu/

NanoCrystal: A Web-Based Crystallographic Tool for the Construction of Nanoparticles Based on Their Crystal Habit

Modeling of nanoparticles is an essential first step to assess their capacities for different uses such as energy storage and drug delivery. However, creating an initial starting conformation for modeling and simulation is tedious because every crystalline material grows with a different crystal habit. In this application note, we describe NanoCrystal, a novel web-based crystallographic tool that creates nanoparticle models from any crystal structure guided by their preferred equilibrium shape under standard conditions according to the Wulff morphology (crystal habit). Users can upload a cif file, define the Miller indices and their corresponding minimum surface energies according to the Wulff construction of a particular crystal, and specify the size of the nanocrystal. As a result, the nanoparticle is constructed and visualized, and the coordinates of the atoms are output to the user. NanoCrystal can be accessed at http://nanocrystal.vi-seem.edu/

NanoCrystal: A Web-Based Crystallographic Tool for the Construction of Nanoparticles Based on Their Crystal Habit

Modeling of nanoparticles is an essential first step to assess their capacities for different uses such as energy storage and drug delivery. However, creating an initial starting conformation for modeling and simulation is tedious because every crystalline material grows with a different crystal habit. In this application note, we describe NanoCrystal, a novel web-based crystallographic tool that creates nanoparticle models from any crystal structure guided by their preferred equilibrium shape under standard conditions according to the Wulff morphology (crystal habit). Users can upload a cif file, define the Miller indices and their corresponding minimum surface energies according to the Wulff construction of a particular crystal, and specify the size of the nanocrystal. As a result, the nanoparticle is constructed and visualized, and the coordinates of the atoms are output to the user. NanoCrystal can be accessed at http://nanocrystal.vi-seem.edu/

NanoCrystal: A Web-Based Crystallographic Tool for the Construction of Nanoparticles Based on Their Crystal Habit

Modeling of nanoparticles is an essential first step to assess their capacities for different uses such as energy storage and drug delivery. However, creating an initial starting conformation for modeling and simulation is tedious because every crystalline material grows with a different crystal habit. In this application note, we describe NanoCrystal, a novel web-based crystallographic tool that creates nanoparticle models from any crystal structure guided by their preferred equilibrium shape under standard conditions according to the Wulff morphology (crystal habit). Users can upload a cif file, define the Miller indices and their corresponding minimum surface energies according to the Wulff construction of a particular crystal, and specify the size of the nanocrystal. As a result, the nanoparticle is constructed and visualized, and the coordinates of the atoms are output to the user. NanoCrystal can be accessed at http://nanocrystal.vi-seem.edu/

NanoCrystal: A Web-Based Crystallographic Tool for the Construction of Nanoparticles Based on Their Crystal Habit

Modeling of nanoparticles is an essential first step to assess their capacities for different uses such as energy storage and drug delivery. However, creating an initial starting conformation for modeling and simulation is tedious because every crystalline material grows with a different crystal habit. In this application note, we describe NanoCrystal, a novel web-based crystallographic tool that creates nanoparticle models from any crystal structure guided by their preferred equilibrium shape under standard conditions according to the Wulff morphology (crystal habit). Users can upload a cif file, define the Miller indices and their corresponding minimum surface energies according to the Wulff construction of a particular crystal, and specify the size of the nanocrystal. As a result, the nanoparticle is constructed and visualized, and the coordinates of the atoms are output to the user. NanoCrystal can be accessed at http://nanocrystal.vi-seem.edu/

NanoCrystal: A Web-Based Crystallographic Tool for the Construction of Nanoparticles Based on Their Crystal Habit

Modeling of nanoparticles is an essential first step to assess their capacities for different uses such as energy storage and drug delivery. However, creating an initial starting conformation for modeling and simulation is tedious because every crystalline material grows with a different crystal habit. In this application note, we describe NanoCrystal, a novel web-based crystallographic tool that creates nanoparticle models from any crystal structure guided by their preferred equilibrium shape under standard conditions according to the Wulff morphology (crystal habit). Users can upload a cif file, define the Miller indices and their corresponding minimum surface energies according to the Wulff construction of a particular crystal, and specify the size of the nanocrystal. As a result, the nanoparticle is constructed and visualized, and the coordinates of the atoms are output to the user. NanoCrystal can be accessed at http://nanocrystal.vi-seem.edu/

FEPrepare: A Web-Based Tool for Automating the Setup of Relative Binding Free Energy Calculations

Relative binding free energy calculations in drug design are becoming a useful tool in facilitating lead binding affinity optimization in a cost- and time-efficient manner. However, they have been limited by technical challenges such as the manual creation of large numbers of input files to set up, run, and analyze free energy simulations. In this Application Note, we describe FEPrepare, a novel web-based tool, which automates the setup procedure for relative binding FEP calculations for the dual-topology scheme of NAMD, one of the major MD engines, using OPLS-AA force field topology and parameter files. FEPrepare provides the user with all necessary files needed to run a FEP/MD simulation with NAMD. FEPrepare can be accessed and used at https://feprepare.vi-seem.eu/

FEPrepare: A Web-Based Tool for Automating the Setup of Relative Binding Free Energy Calculations

Relative binding free energy calculations in drug design are becoming a useful tool in facilitating lead binding affinity optimization in a cost- and time-efficient manner. However, they have been limited by technical challenges such as the manual creation of large numbers of input files to set up, run, and analyze free energy simulations. In this Application Note, we describe FEPrepare, a novel web-based tool, which automates the setup procedure for relative binding FEP calculations for the dual-topology scheme of NAMD, one of the major MD engines, using OPLS-AA force field topology and parameter files. FEPrepare provides the user with all necessary files needed to run a FEP/MD simulation with NAMD. FEPrepare can be accessed and used at https://feprepare.vi-seem.eu/

FEPrepare: A Web-Based Tool for Automating the Setup of Relative Binding Free Energy Calculations

Relative binding free energy calculations in drug design are becoming a useful tool in facilitating lead binding affinity optimization in a cost- and time-efficient manner. However, they have been limited by technical challenges such as the manual creation of large numbers of input files to set up, run, and analyze free energy simulations. In this Application Note, we describe FEPrepare, a novel web-based tool, which automates the setup procedure for relative binding FEP calculations for the dual-topology scheme of NAMD, one of the major MD engines, using OPLS-AA force field topology and parameter files. FEPrepare provides the user with all necessary files needed to run a FEP/MD simulation with NAMD. FEPrepare can be accessed and used at https://feprepare.vi-seem.eu/