Tutorials And Protocols

Upon completion of MDS you will find the analysis files generated under the 800 sim files. There will be two files of data titled analysis.tab & analysisRes.tab. Analysis.tab uses root-mean square deviation to track the global movement of the carbon-alpha...

This protocol will describe the steps to connect two pieces of a protein model together.  You may have a portion of the protein created by homology modeling in YASARA and an additional portion created by threading with I-TASSER, or maybe two portions of the model from...

Molecular dynamics is a simulation methodology often used for studying the conformational rearrangements of molecules and their interactions with other molecular species in a range of environments. Potential applications include variant analysis, ligand docking, and...

Homology modeling is a procedure that generates a previously unknown protein structure by “fitting” its sequence (target) into a known structure (template), given a certain level of sequence homology (at least 30%) between target and template. This step lays the...

Changing one or more amino acids allows you to visualize the structural change of a variant, as well as to analyze the potential perturbation by performing a molecular dynamics simulation. Changing Amino Acids of a Protein Protocol (Click Link to Download PDF)

This method uses Ray-Trace Screen Capturing to trick the computer into thinking the screen is much larger than it actually is. This leaves you with a very high DPI image. Creating a High Quality Screenshot (Click Link to Download PDF)

The alignment of 2 or more proteins is a visualization method that can be used to assess the structural differences between either 2 different proteins, or a wild-type compared to a protein with variants. Alignment of 2 Proteins Protocol (Please Click to Download...

This tutorial will break down how to perform MDS on Transmembrane Proteins. You will have the option to customize your lipid membrane to your choosing, or to run based on the default settings that we have in place. Transmembrane Protein MDS (Click Link to Download...

Manually adding amino acids allows you the flexibility to build missing portions of a protein. Be cautious as these added amino acids may not be in the ideal conformation. Perform an energy minimization to return ideal structural conformation.  Adding Amino Acids to A...