Molecular Probes Guide (Hybrid Solvent Inserter)
Table of Contents
Molecular Probes Guide (Hybrid Solvent Inserter)
In mixed-solvent molecular dynamics (MixMD) simulations, a rational combination of different molecular probes greatly enhances the detection of cryptic pockets and potential binding hotspots in biomolecules. This guide summarizes the properties, classifications.
MixMD System Builder is a web-based application for generating mixed-solvent molecular simulation systems. It supports protein structure upload, flexible probe selection, box configuration, and automatic topology generation. Users can easily integrate custom molecules and apply optional solvation and ionization, resulting in ready-to-use simulation packages. I redeployed this online tool in my repository and you can use this tool for free by clicking here.
Probe GridMap Builder is a local web-based software interface designed to analyze molecular dynamics (MD) trajectories in .trr or .nc format, powered by the AMBER cpptraj backend. It enables users to generate grid-based interaction maps between protein structures and solvent probe atoms across dynamic frames. You can use this tool for free by clicking here. 👉 Live Demo
Principles of Usage Instructions for Single probe
This table summarizes the molecular weight and density information of 13 commonly used molecular probes.
| Probe |
Molecular Weight (g/mol) |
Density (g/mL) |
| formamide |
45.041 |
1.13 |
| dmso |
78.129 |
1.10 |
| meoh (methanol) |
32.042 |
0.791 |
| isopropanol |
60.096 |
0.785 |
| acetonitrile |
41.053 |
0.786 |
| guanidinium |
60.080 |
1.260 |
| acetate |
59.044 |
1.0492 |
| n-methylacetamide |
73.095 |
0.957 |
| benzene |
78.114 |
0.874 |
| toluene |
92.141 |
0.867 |
| phenol |
94.113 |
1.071 |
| indole |
117.151 |
1.220 |
| pyrimidine |
80.090 |
1.016 |
Notes
-
Guanidinium:
Pure guanidinium cation density is unavailable; estimated based on typical guanidinium chloride solution density (~1.26 g/mL). Can detect negatively charged regions on protein surfaces (such as near Asp and Glu residues)
-
Acetate:
As pure acetate ion density is not measurable directly, acetic acid (CH₃COOH) liquid density (~1.0492 g/mL) is used as an approximation. Can detect positively charged regions on protein surfaces (such as near LyS and Arg residues)
Special Notes
- Electric neutral system: If many charged small molecules are added, additional Na * and CI ions must be added in the simulation to balance the overall charge
- Short range exclusion: A small amount of random dispersion can be added to the initial distribution of probes to prevent excessive stacking
- Minimize energy: After adding the probe, it is very important to perform a rigorous round of restrained minimization!
Features:
- Extremely strong polarity
- Excellent hydrogen bond donor
- Small molecule size, easy to penetrate narrow pockets
Suitable Environments:
- Polar active sites
- Hidden polar crevices or grooves
Combination Suggestions:
- Combine with meoh and n-methylacetamide to enhance detection of polar pockets.
dmso
Features:
- Highly polar and highly soluble
- Penetrates both hydrophobic and polar regions
- Compatible with diverse environments
Suitable Environments:
- Mixed hydrophobic-polar surfaces
- Deeply hidden cryptic pockets
Combination Suggestions:
- Combine with benzene and isopropanol to maximize overall detection coverage.
meoh
Features:
- Moderate polarity
- Excellent hydrogen bond donor and acceptor
- Small size for fine pocket detection
Suitable Environments:
- Small polar surface pockets
- Hydration sites or narrow clefts
Combination Suggestions:
- Use with formamide or guanidinium to strengthen polar detection.
isopropanol
Features:
- Moderate hydrophobicity
- Capable of hydrogen bonding
- Small and flexible molecule
Suitable Environments:
- Small hydrophobic pockets
- Mixed polarity regions
Combination Suggestions:
- Pair with benzene or toluene to cover hydrophobic surfaces.
acetonitrile
Features:
- Weak polarity
- Small size, fast diffusion
- Limited hydrogen bonding capacity
Suitable Environments:
- Neutral or weakly polar surfaces
- Gas-phase like hidden cavities
Combination Suggestions:
- Can be used alone or paired with isopropanol for broader coverage.
guanidinium
Features:
- Positively charged probe
- Strong ability to stabilize ion pairs
- Excellent hydrogen bond donor
Suitable Environments:
- Surfaces rich in negative charges
- DNA/RNA binding sites
- Acidic residue clusters (Glu, Asp)
Combination Suggestions:
- Combine with acetate (negative charge probe) for complementary charge detection.
acetate
Features:
- Negatively charged probe
- Mimics anionic environments
- Good hydration properties
Suitable Environments:
- Surfaces rich in positive charges
- Basic residue clusters (Lys, Arg)
Combination Suggestions:
- Use with guanidinium for complementary charge pair detection.
n-methylacetamide
Features:
- Moderate polarity
- Mimics peptide backbone (CONH)
- Participates in hydrogen bond networks
Suitable Environments:
- Cryptic sites involved in peptide backbone recognition
- Protein-protein interface pockets
Combination Suggestions:
- Combine with formamide to enhance hydrogen bond network probing.
benzene
Features:
- Classic hydrophobic aromatic probe
- Nonpolar
- Small size, suitable for small cavity filling
Suitable Environments:
- Hydrophobic patches
- Aromatic stacking regions (Phe, Tyr, Trp clusters)
Combination Suggestions:
- Combine with isopropanol to extend hydrophobic detection.
toluene
Features:
- Strong aromaticity
- Slightly larger than benzene
- Stronger hydrophobicity
Suitable Environments:
- Deep hydrophobic pockets
- Hydrophobic cavities or clefts
Combination Suggestions:
- Combine with benzene and indole to cover cavities of different sizes.
phenol
Features:
- Aromatic molecule with weak polarity (hydroxyl group)
- Can participate in both hydrophobic and hydrogen bonding interactions
Suitable Environments:
- Polar-hydrophobic interface areas
- Mildly polar aromatic pockets
Combination Suggestions:
- Combine with benzene and meoh for enhanced interface detection.
indole
Features:
- Large aromatic probe
- Mimics tryptophan side chains (Trp)
- Supports stacking, hydrogen bonding, and hydrophobic interactions
Suitable Environments:
- Large aromatic cryptic pockets
- Deep-core pocket exploration
Combination Suggestions:
- Combine with benzene and toluene for comprehensive aromatic stacking detection.
pyrimidine
Features:
- Nitrogen-containing aromatic ring
- Moderate polarity, weak hydrogen bond acceptor
Suitable Environments:
- Aromatic-polar interface regions
- Small-molecule binding site identification
Combination Suggestions:
- Combine with indole and benzene for detailed detection of aromatic stacking or polar stacking regions.
Conclusion
Rational combination of molecular probes significantly improves the efficiency of cryptic pocket and hotspot detection.
This strategy is a critical step in advanced simulation methods such as MixMD, FEP, and FragMap, providing vital insights for structure-based drug discovery. Scientific selection and combination of molecular probes can significantly improve the efficiency of cryptic pocket detection, providing a solid structural foundation for drug discovery and target validation.