ProMS – Molecular Sense

Scientific Research

Proms

Protein Molecular Surface Calculator

ProMS, the protein molecular surface calculator, is an integrated application that was developed to calculate and visualize molecular surface properties. The software is available to download free of charge for those interested. For access to the source code and documentation, please contact the lab.

The precursor to ProMS was PSPC (Protein Surface Property Calculator, 2003). ProMS development began in 2021 to update the software and provide additional functionality and features (read more below). For more information pertaining to PSPC, read here.

Molecular Surfaces

Molecular surfaces play an integral role in many biological processes. They are involved in protein folding, protein-protein interactions, molecular recognition, molecular docking, signaling, and more. In 1983, Michael Connolly developed an algorithm to generate the geometrical molecular surface of any protein given as in input.

In simple terms, the “Connolly surface” is generated by rolling an imaginary sphere over the 3D structure of the molecule. The output surface is thus a function of the sphere’s radius (also referred to as the probe radius). To this day, Connolly’s algorithm remains the most popular analytical method for mapping protein surfaces.

ProMS Features

For a more detailed summary of ProMS’ features, please reference the user manual.

Surface property calculations
- Computations derived from Connolly’s msRoll and Nicolau’s work on atomic hydrophobicities
- “Under the hood” – complexity and tediousness is hidden by the intuitive GUI
- Multiple output file formats, including a .mov file if visualization is enabled
- A sample of the output in tabular form can be found below

Choice of various input parameters
- PDB ID, probe radius (1.4-20A), pH, hydrophobicity scale
- Computations via Method 1 or Method 2 at either atomic or amino acid resolution

Integration within PyMOL & design of custom visualization modules
- ProMS is an extension of Schrodinger’s PyMOL, an open-source molecular manipulation tool
- Design of custom modules allows for the visualization of Nicolau’s hydrophobicity algorithms for any protein

Batch mode
- Enables the analysis of several proteins / different parameters at the click of a single button

Custom PDB integration
- Supports PDBs that have been modified by the user or that have not yet been published to an online database

ProMS Sample Output

Below is a sample of the properties calculated by ProMS, aggregated into a table. The analyzed proteins correspond to the same proteins chosen for the BAD project. These properties were calculated using Nicolau’s Method 1 and the “Dgwif” hydrophobicity scale. There are four copies of each PDB because the probe radius (1.4A vs 20A) and the resolution (atomic vs amino acid) were changed (see last two columns).

The majority of the output columns are self-explanatory. However, some of the secondary properties, such as density, specific density, and area extent are less intuitive.

Density = total charge or hydrophobicity / total area
Specific density = total charge or hydrophobicity / total charged area or hydrophobic area
Area extent = charged or hydrophobic area / total area
All areas are in units of square Angstroms

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ID	PDB	Probe Radius	Resolution	Total Surface Area	Positive Area	Negative Area	Hydrophobic Area	Hydrophilic Area	Total Positive Charge	Total Negative Charge	Total Hydrophobicity	Total Hydrophilicity	Positive Charge Density	Positive Charge Specific Density	Negative Charge Density	Negative Charge Specific Density	Positive Area Extent	Negative Area Extent	Hydrophobic Density	Hydrophobic Specific Density	Hydrophilic Density	Hydrophilic Specific Density	Hydrophobic Area Extent	Hydrophilic Area Extent

ID	PDB	Probe Radius	Resolution	Total Surface Area	Positive Area	Negative Area	Hydrophobic Area	Hydrophilic Area	Total Positive Charge	Total Negative Charge	Total Hydrophobicity	Total Hydrophilicity	Positive Charge Density	Positive Charge Specific Density	Negative Charge Density	Negative Charge Specific Density	Positive Area Extent	Negative Area Extent	Hydrophobic Density	Hydrophobic Specific Density	Hydrophilic Density	Hydrophilic Specific Density	Hydrophobic Area Extent	Hydrophilic Area Extent
1	1A4V	1.4	AT	7834	827	4150	2050	2927	34	-87	-252	114	0.0044	0.0412	-0.0112	-0.0211	0.1056	0.5297	-0.0321	-0.1228	0.0146	0.0390	0.2617	0.3736
2	1A4V	20.0	AT	4690	1126	3416	2878	1664	42	-65	-239	21	0.0089	0.0373	-0.0139	-0.0191	0.2400	0.7284	-0.0509	-0.0830	0.0045	0.0127	0.6136	0.3548
3	1AO6	1.4	AA	55064	9597	45467	45374	8150	28	-120	-387	49	0.001	0.003	-0.002	-0.003	0.174	0.826	-0.007	-0.009	0.001	0.006	0.824	0.148
4	1AO6	1.4	AT	55064	9597	45467	22081	32983	395	-974	-2980	1465	0.007	0.041	-0.018	-0.021	0.174	0.826	-0.054	-0.135	0.027	0.044	0.401	0.599
5	1AO6	20.0	AA	26983	6381	20601	26756	179	43	-94	-301	1	0.002	0.007	-0.003	-0.005	0.236	0.764	-0.011	-0.011	0	0.006	0.992	0.007
6	1AO6	20.0	AT	26983	6094	20451	18764	7781	280	-413	-1677	96	0.01	0.046	-0.015	-0.02	0.226	0.758	-0.062	-0.089	0.004	0.012	0.695	0.288
7	1B0L	1.4	AA	28019	6418	21601	23691	3892	13	-59	-162	24	0	0.002	-0.002	-0.003	0.229	0.771	-0.006	-0.007	0.001	0.006	0.846	0.139
8	1B0L	1.4	AT	28019	6418	21601	12789	15230	181	-458	-1672	789	0.006	0.028	-0.016	-0.021	0.229	0.771	-0.06	-0.131	0.028	0.052	0.456	0.544
9	1B0L	20.0	AA	16486	5756	10729	16302	130	17	-42	-140	0	0.001	0.003	-0.003	-0.004	0.349	0.651	-0.009	-0.009	0	0.007	0.989	0.008
10	1B0L	20.0	AT	16486	5632	10260	10856	5037	118	-183	-897	66	0.007	0.021	-0.011	-0.018	0.342	0.622	-0.054	-0.083	0.004	0.013	0.658	0.306

Showing 1 to 10 of 90 entries

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Additional Output

In addition to the properties above, ProMS also outputs detailed area calculations and the solvent-excluded volume via Connolly’s msRoll. Furthermore, using the protein’s molecular weight from literature, an atomic volume can also be calculated. Lastly, sphericity, monolayer volume density, and monolayer weight can all be computed from the aforementioned values. The results can be found in the table below.

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ID	Protein	PDB	Probe Radius	Molecular Weight	Atomic Volume	Contact Area	Reentrant Area	Molecular Area	Accessible Area	Solvent-Excluded Volume	Sphericity	Monolayer Volume Density	Monolayer Weight
1	Alpha-2-macroglobulin	6TAV	1.4	666.20	746144	70808	169367	240174	225522	669383	0.1541	0.0922	1.3815
2	Alpha-2-macroglobulin	6TAV	20.0	666.20	746144	1262	89101	90363	141849	1405237	0.6714	0.5628	5.1454
3	Alpha-amylase	1PIF	1.4	55.47	62126	5451	11742	17193	17508	64675	0.4532	0.4194	2.4863
4	Alpha-amylase	1PIF	20.0	55.47	62126	218	11138	11356	33308	90497	0.8584	0.6000	2.8432
5	Alpha-chymotrypsin	1CHO	1.4	31.29	35045	3795	7602	11396	12193	35672	0.4598	0.4256	2.1162
6	Alpha-chymotrypsin	1CHO	20.0	31.29	35045	170	7576	7746	26385	52972	0.8806	0.6025	2.3014
7	Alpha-lactalbulmin	1A4V	1.4	14.17	15870	2217	3926	6142	7090	16266	0.5054	0.4653	1.7686
8	Alpha-lactalbulmin	1A4V	20.0	14.17	15870	132	4557	4690	20530	24158	0.8617	0.6004	1.7530
9	Beta-lactoglobulin	3BLG	1.4	18.32	20518	2554	4916	7470	8179	21956	0.5076	0.4671	1.8791
10	Beta-lactoglobulin	3BLG	20.0	18.32	20518	141	5276	5418	21829	31373	0.8879	0.6033	1.9133

Showing 1 to 10 of 36 entries

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Software Specifications

ProMS is written in Python 3
- Makes heavy use of Pandas & Tkinter modules
Extends Schrodinger’s PyMOL as a “plugin” that can be installed via their main application
Uses Michael Connolly’s msRoll.exe program to compute the molecular surface (part of his molecular surface package)
Selected protein outputs have been stored in the same MySQL database as BAD