MxMD Cosolvent Probes

The default cosolvent probes are shown in Table 1. These cosolvents were chosen because they are water-miscible and are known to mix evenly in MxMD simulations without phase separation [3]. Note that these probes are optimized for detecting protein hotspots. For DNA/RNA targets, you might want to use MxMD Custom Cosolvent Probes.

The MxMD workflow also supports immiscible probes. The allowed immiscible probes are listed in Table 2.

Each probe includes ten distinct pre-equilibrated solvent boxes that are used to assemble the initial cosolvent systems.

Table 1. Miscible cosolvent probes for MxMD. Default probes are acetonitrile, isopropanol, and pyrimidine (their names are highlighted in bold).

Name	PDB Residue Type	2D Structure	Chemical Formula	Mapping Role
Acetaldehyde	ACD		C₂H₄O	Polar; H-bond acceptor
Acetamide	ACM		C₂H₅NO	Polar; H-bond acceptor/donor
Acetic Acid	ACY		C₂H₄O₂	Polar; H-bond acceptor/donor
Acetone	ACN		C₃H₆O	Polar; H-bond acceptor
Acetonitrile	CCN		C₂H₃N	Polar; amphipathic
Diethylamine	DME		C₄H₁₁N	H-bond donor; amphipathic
Dimethylsulfoxide / DMSO	DMS		C₂H₆OS	Polar; H-bond acceptor
Ethanol	EOH		C₂H₆O	Polar; H-bond donor
Formamide	ARF		CH₃NO	Polar; H-bond acceptor/donor
Glycerol	GOL		C₃H₈O₃	Polar; H-bond donor
Imidazole	IMD		C₃H₄N₂	5-membered polar aromatic
Isopropanol	IPA		C₃H₈O	H-bond donor/acceptor; small hydrophobic
Isopropylamine	ISP		C₃H₉N	H-bond donor; small hydrophobic
Methylamine	NME		C₁H₅N	Small hydrophobic
Methylsulfonylmethane/DMSO2	7SU		C₂H₆O₂S	Polar; H-bond acceptor
Morpholine	6LR		C₄H₉NO	6-membrane; polar
N-Methylacetamide	NML		C₃H₇ON	Protein backbone-like
Oxazole	OXZL		C₃H₃NO	5-membered aromatic; polar
Oxiranemethanol	OX9		C₃H₆O₂	3-membered aliphatic; H-bond donor/acceptor
Piperidine	PIP		C₅H₁₁N₁	6-membered aliphatic; H-bond donor
Pyrazine	1P4		C₄H₄N₂	6-membered aromatic
Pyridazine	1P2		C₄H₄N₂	6-membered aromatic
Pyridine	PYR		C₅H₅N₁	6-membered aromatic
Pyrimidine	P1R		C₄H₄N₂	6-membered aromatic
Resorcinol	RCO		C₆H₆O₂	H-bond donor/acceptor; 6-membered aromatic
Sulfamide	FUS		H₄N₂O₂S	Polar; H-bond donor/acceptor
Thiazole	THZL		C₃H₃NS	5-membered aromatic
Trifluoroethanol	TFE		C₂H₃F₃O	Polar; H-bond donor/acceptor
Triethylamine	TME		C₆H₁₅N	Small hydrophobic
Urea	URE		CH₄N₂O	Polar; H-bond donor/acceptor

Table 2. Immiscible cosolvent probes for MxMD.

Probe Name	PDB Residue Type
1,3-Oxazinan-2-one	OX2
1-Methyl-1H-Indazole	MI1
1-Naphthol	1NP
1H-Indazole	LZ1
2-Cyanophenol	0R0
2-Methyl-2H-Indazole	MI2
2-Naphthol	2NP
2H-Indazole	LZ2
3-Cyanophenol	0R3
4-Cyanophenol	0R4
Androstenol	AND
Benzene	BNZ
Benzothiazole	BZL
Cyanobenzene	B1X
Furan	FUR
Isatin	ISN
Isobutane	ISB
Isonicotinonitrile	4NN
Isoquinoline	ISQ
Isoquinolinone1	IQ1
Isoquinolinone2	IQ2
Nicotinonitrile	3NN
Oxane	OXA
Oxirane	OXO
Phenol	IHP
Picolinonitrile	2NN
Propyne	PYN
Quinoline	QNL