When working with large molecular simulations or complex molecular assemblies, finding the right subset of molecules can sometimes feel like searching for a needle in a haystack. Whether you want to focus on molecules with a specific number of chains,…
Designing carbon nanotubes (CNTs) for molecular modeling or material science simulations often requires a deep understanding of their structure: the famous n and m parameters that define both the chirality and radius of a CNT. But what if you just…
Have you ever needed to prepare a molecular animation to illustrate how a ligand unbinds from its receptor? This step, while seemingly simple, is often time-consuming and prone to inconsistencies. Whether you’re creating a teaching video, preparing a conference talk,…
For molecular modelers working with computationally intensive tasks like protein structure prediction or molecular dynamics, accessing sufficient computing power is often a challenge. Long simulations, resource-heavy algorithms, and multi-step workflows can overwhelm local computers or delay projects. This is where…
Controlling the timing of when molecular elements appear in a presentation or a movie can be tricky. Whether you’re building a video for a publication, crafting an educational animation, or presenting your research, ensuring that molecular fragments appear precisely when…
Designing nanotube-based nanodevices or studying their properties often means building precise atomic models, which can be a time-consuming task. If you’ve worked in nanotechnology, molecular transport modeling, or material science, you’re probably familiar with the repetitive steps needed to create…
One common challenge in molecular modeling is adapting molecular structures when atoms move during a simulation. Often, manually updating topologies like covalent bonds and atom types can slow down workflows and increase the chance of errors. If you’ve ever tried…
One common challenge when studying macromolecules is understanding and predicting how biomolecular structures open and close their active or binding sites. Whether you’re designing a drug or investigating conformational transitions, this dynamic behavior is crucial — but simulating it can…
Working with dozens (or hundreds) of PDB files can be a common challenge in computational biology and drug discovery. Whether you’re screening compounds, running molecular dynamics, or preparing datasets for machine learning, there’s one recurring issue: curating and prepping all…
When telling the story of a complex molecular system, timing and visual consistency can have a significant impact on comprehension. Many researchers and educators rely on animations to construct engaging molecular presentations. However, a common challenge arises when trying to…
