ProMS – BIOLOGICAL MICROFLUIDICS

Protein Molecular Surface Calculator

The Protein Molecular Surface Calculator (ProMS) is a

PyMOL-integrated computational tool designed to quantify and visualize physicochemical properties of molecular surfaces at atomic and residue resolution. ProMS enables users to analyze how proteins, nucleic acids, and small molecules interact with their environment by mapping key surface properties such as hydrophobicity and charge.

ProMS was initially released in 2022 and has since been updated with expanded functionality, improved stability, and enhanced integration within PyMOL. For access to the source code, please contact the lab.

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.

In 1993, Connolly released software to encapsulate his algorithms for practical purposes. ProMS uses a portion of this software (notably msRoll.exe) as a step in calculating protein surface properties. Additionally, ProMS applies Nicolau’s work to investigate molecular surfaces at the atomic and amino acid resolution. This methodology provides a more accurate and higher-resolution description of the protein surface. Read more about it here.

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 .pse (PyMOL session) 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
  - Custom force fields and atom types
  - Highly adaptive custom visualization module

- Integration within PyMOL
  - ProMS is an extension of Schrodinger’s PyMOL, an open-source molecular manipulation tool
  - Easy-to-install plugin at the click of a few buttons

- Batch mode
  - Enables the analysis of several proteins / different parameters at once

- 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

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
11	1BJ5	1.4	AT	28109	4632	23148	10537	17244	183	-477	-1283	674	0.0065	0.0395	-0.0170	-0.0206	0.1648	0.8235	-0.0456	-0.1218	0.0240	0.0391	0.3748	0.6135
12	1BJ5	20.0	AT	15875	2496	12338	9348	5486	90	-239	-759	50	0.0057	0.0362	-0.0151	-0.0194	0.1572	0.7772	-0.0478	-0.0812	0.0031	0.0091	0.5888	0.3456
13	1BUW	1.4	AA	25381	4068	21272	20142	5065	11	-52	-107	32	0	0.003	-0.002	-0.002	0.16	0.838	-0.004	-0.005	0.001	0.006	0.794	0.2
14	1BUW	1.4	AT	25381	4068	21272	8939	16401	156	-407	-1198	835	0.006	0.038	-0.016	-0.019	0.16	0.838	-0.047	-0.134	0.033	0.051	0.352	0.646
15	1BUW	20.0	AA	12702	3295	9407	11546	1156	18	-35	-72	6	0.001	0.005	-0.003	-0.004	0.259	0.741	-0.006	-0.006	0.001	0.006	0.909	0.091
16	1BUW	20.0	AT	12702	3283	9374	6547	6110	129	-167	-601	77	0.01	0.039	-0.013	-0.018	0.258	0.738	-0.047	-0.092	0.006	0.013	0.515	0.481
17	1CF3	1.4	AA	20897	4096	16801	16586	4244	7	-47	-109	25	0	0.002	-0.002	-0.003	0.196	0.804	-0.005	-0.007	0.001	0.006	0.794	0.203
18	1CF3	1.4	AT	20897	4096	16801	9462	11435	121	-358	-1237	595	0.006	0.03	-0.017	-0.021	0.196	0.804	-0.059	-0.131	0.029	0.052	0.453	0.547
19	1CF3	20.0	AA	12549	3100	9382	11900	648	11	-42	-104	4	0.001	0.004	-0.003	-0.005	0.247	0.748	-0.008	-0.009	0	0.006	0.948	0.052
20	1CF3	20.0	AT	12549	2994	9221	9049	3166	85	-173	-764	40	0.007	0.028	-0.014	-0.019	0.239	0.735	-0.061	-0.084	0.003	0.013	0.721	0.252
21	1CHO	1.4	AT	11913	1636	5805	3375	4066	49	-125	-367	192	0.0041	0.0301	-0.0105	-0.0216	0.1373	0.4873	-0.0308	-0.1089	0.0161	0.0472	0.2833	0.3413
22	1CHO	20.0	AT	7746	1705	5630	4736	2599	46	-91	-310	18	0.0060	0.0271	-0.0118	-0.0162	0.2201	0.7269	-0.0400	-0.0654	0.0023	0.0069	0.6114	0.3356
23	1GPE	1.4	AT	31439	4366	17130	9387	12109	157	-366	-1105	484	0.0050	0.0360	-0.0116	-0.0214	0.1389	0.5449	-0.0351	-0.1177	0.0154	0.0400	0.2986	0.3852
24	1GPE	20.0	AT	20175	5125	14374	11437	8061	139	-241	-810	59	0.0069	0.0272	-0.0119	-0.0167	0.2540	0.7124	-0.0402	-0.0708	0.0029	0.0074	0.5669	0.3996
25	1HLS	1.4	AT	3137	590	2548	1859	1278	15	-51	76	-152	0.0047	0.0248	-0.0162	-0.0199	0.1880	0.8120	0.0243	0.0410	-0.0483	-0.1187	0.5927	0.4073
26	1HLS	20.0	AT	2648	472	2162	1615	1018	6	-37	-106	12	0.0021	0.0121	-0.0139	-0.0170	0.1781	0.8163	-0.0402	-0.0659	0.0045	0.0117	0.6100	0.3845
27	1HML	1.4	AA	6097	1103	4993	4271	1694	2	-13	-36	8	0	0.003	-0.002	-0.003	0.181	0.819	-0.006	-0.009	0.001	0.005	0.701	0.278
28	1HML	1.4	AT	6097	1103	4993	2581	3515	43	-107	-354	189	0.007	0.04	-0.018	-0.022	0.181	0.819	-0.058	-0.137	0.031	0.054	0.423	0.577
29	1HML	20.0	AA	4692	1112	3536	3805	886	5	-13	-38	4	0.001	0.005	-0.003	-0.004	0.237	0.754	-0.008	-0.01	0.001	0.005	0.811	0.189
30	1HML	20.0	AT	4692	1100	3371	2940	1531	44	-61	-267	20	0.009	0.04	-0.013	-0.018	0.235	0.718	-0.057	-0.091	0.004	0.013	0.627	0.326
31	1HRC	1.4	AA	5479	1038	4440	4573	830	3	-11	-34	4	0.001	0.004	-0.002	-0.003	0.19	0.81	-0.006	-0.008	0.001	0.006	0.835	0.152
32	1HRC	1.4	AT	5479	1038	4440	2311	3167	42	-92	-273	104	0.008	0.041	-0.017	-0.021	0.19	0.81	-0.05	-0.118	0.019	0.033	0.422	0.578
33	1HRC	20.0	AA	3973	1288	2639	3831	141	8	-10	-33	0	0.002	0.007	-0.003	-0.004	0.324	0.664	-0.008	-0.009	0	0.003	0.964	0.036
34	1HRC	20.0	AT	3973	1279	2605	2477	1406	56	-46	-191	11	0.014	0.044	-0.012	-0.018	0.322	0.656	-0.048	-0.077	0.003	0.008	0.624	0.354
35	1IGT	1.4	AA	59573	12441	47131	47611	10947	24	-132	-279	61	0	0.002	-0.002	-0.003	0.209	0.791	-0.005	-0.006	0.001	0.006	0.799	0.184
36	1IGT	1.4	AT	59573	12441	47131	26382	33191	343	-984	-3121	1799	0.006	0.028	-0.017	-0.021	0.209	0.791	-0.052	-0.118	0.03	0.054	0.443	0.557
37	1IGT	20.0	AA	37314	9291	27977	32794	3493	35	-111	-215	20	0.001	0.004	-0.003	-0.004	0.249	0.75	-0.006	-0.007	0.001	0.006	0.879	0.094
38	1IGT	20.0	AT	37314	8820	27129	23247	12702	229	-479	-1502	160	0.006	0.026	-0.013	-0.018	0.236	0.727	-0.04	-0.065	0.004	0.013	0.623	0.34
39	1M1J	1.4	AT	88145	18119	68552	37073	49597	580	-1441	-4183	1947	0.0066	0.0320	-0.0164	-0.0210	0.2056	0.7777	-0.0475	-0.1128	0.0221	0.0393	0.4206	0.5627
40	1M1J	20.0	AT	55493	15143	38709	33059	20793	400	-673	-2240	222	0.0072	0.0264	-0.0121	-0.0174	0.2729	0.6976	-0.0404	-0.0677	0.0040	0.0107	0.5957	0.3747
41	1PIF	1.4	AA	17193	4104	13089	13474	3528	7	-36	-79	27	0	0.002	-0.002	-0.003	0.239	0.761	-0.005	-0.006	0.002	0.008	0.784	0.205
42	1PIF	1.4	AT	17193	4104	13089	7955	9237	99	-279	-919	388	0.006	0.024	-0.016	-0.021	0.239	0.761	-0.053	-0.116	0.023	0.042	0.463	0.537
43	1PIF	20.0	AA	11355	3023	8331	10058	1242	7	-31	-63	11	0.001	0.003	-0.003	-0.004	0.266	0.734	-0.006	-0.006	0.001	0.01	0.886	0.109
44	1PIF	20.0	AT	11355	2954	8058	6666	4346	65	-133	-469	46	0.006	0.022	-0.012	-0.017	0.26	0.71	-0.041	-0.07	0.004	0.011	0.587	0.383
45	2CHA	1.4	AA	19010	4537	14473	15317	3341	8	-41	-74	22	0	0.002	-0.002	-0.003	0.239	0.761	-0.004	-0.005	0.001	0.007	0.806	0.176
46	2CHA	1.4	AT	19010	4537	14473	8549	10461	118	-299	-935	519	0.006	0.026	-0.016	-0.021	0.239	0.761	-0.049	-0.109	0.027	0.05	0.45	0.55
47	2CHA	20.0	AA	11137	4534	6490	10388	468	18	-27	-63	2	0.002	0.004	-0.003	-0.004	0.407	0.583	-0.006	-0.006	0	0.006	0.933	0.042
48	2CHA	20.0	AT	11137	4276	6475	7445	3305	116	-106	-472	15	0.01	0.027	-0.01	-0.016	0.384	0.581	-0.042	-0.064	0.001	0.005	0.669	0.297
49	2LYZ	1.4	AA	5796	1616	4179	4667	1001	2	-11	-25	7	0	0.002	-0.002	-0.003	0.279	0.721	-0.004	-0.005	0.001	0.007	0.805	0.173
50	2LYZ	1.4	AT	5796	1616	4179	2658	3138	36	-84	-335	196	0.006	0.023	-0.015	-0.02	0.279	0.721	-0.058	-0.126	0.034	0.063	0.459	0.541
51	2LYZ	20.0	AA	4489	2014	2449	4192	251	4	-9	-23	1	0.001	0.002	-0.002	-0.004	0.449	0.546	-0.005	-0.006	0	0.006	0.934	0.056
52	2LYZ	20.0	AT	4489	2014	2372	3164	1223	29	-35	-243	13	0.006	0.014	-0.008	-0.015	0.449	0.528	-0.054	-0.077	0.003	0.011	0.705	0.272
53	2RCJ	1.4	AT	312775	0	312775	0	312775	0	-4805	0	3227	0.0000	0.0000	-0.0154	-0.0154	0.0000	1.0000	0.0000	0.0000	0.0103	0.0103	0.0000	1.0000
54	2RCJ	20.0	AT	168174	0	36468	0	36468	0	-376	0	235	0.0000	0.0000	-0.0022	-0.0103	0.0000	0.2168	0.0000	0.0000	0.0014	0.0064	0.0000	0.2168
55	3BLG	1.4	AA	7470	1277	6192	5829	1589	3	-16	-48	7	0.001	0.003	-0.002	-0.003	0.171	0.829	-0.006	-0.008	0.001	0.005	0.78	0.213
56	3BLG	1.4	AT	7470	1277	6192	3118	4351	53	-133	-430	224	0.007	0.042	-0.018	-0.022	0.171	0.829	-0.058	-0.138	0.03	0.051	0.417	0.583
57	3BLG	20.0	AA	5417	1284	4068	4961	456	7	-16	-50	2	0.001	0.006	-0.003	-0.004	0.237	0.751	-0.009	-0.01	0	0.004	0.916	0.084
58	3BLG	20.0	AT	5417	1281	3989	3385	1885	49	-75	-306	22	0.009	0.039	-0.014	-0.019	0.236	0.736	-0.056	-0.09	0.004	0.012	0.625	0.348
59	3GHG	1.4	AA	91878	19446	72356	69525	20575	41	-185	-457	117	0	0.002	-0.002	-0.003	0.212	0.788	-0.005	-0.007	0.001	0.006	0.757	0.224
60	3GHG	1.4	AT	91878	19446	72356	37185	54617	599	-1487	-4754	2689	0.007	0.031	-0.016	-0.021	0.212	0.788	-0.052	-0.128	0.029	0.049	0.405	0.594
61	3GHG	20.0	AA	55851	18845	36805	44127	10904	66	-130	-332	65	0.001	0.004	-0.002	-0.004	0.337	0.659	-0.006	-0.008	0.001	0.006	0.79	0.195
62	3GHG	20.0	AT	55851	18001	35344	33742	19603	444	-588	-2640	248	0.008	0.025	-0.011	-0.017	0.322	0.633	-0.047	-0.078	0.004	0.013	0.604	0.351
63	3M7P	1.4	AA	15314	3187	12126	11479	3425	4	-31	-69	20	0	0.002	-0.002	-0.003	0.208	0.792	-0.005	-0.006	0.001	0.006	0.75	0.224
64	3M7P	1.4	AT	15314	3187	12126	6743	8571	86	-248	-874	551	0.006	0.027	-0.016	-0.02	0.208	0.792	-0.057	-0.13	0.036	0.064	0.44	0.56
65	3M7P	20.0	AA	10102	2600	7501	7723	2270	4	-26	-54	13	0	0.002	-0.003	-0.003	0.257	0.743	-0.005	-0.007	0.001	0.006	0.765	0.225
66	3M7P	20.0	AT	10102	2212	7096	5691	3618	30	-115	-466	45	0.003	0.014	-0.011	-0.016	0.219	0.702	-0.046	-0.082	0.004	0.013	0.563	0.358
67	3RGK	1.4	AA	7215	1326	5888	6006	1208	4	-15	-48	6	0.001	0.003	-0.002	-0.003	0.184	0.816	-0.007	-0.008	0.001	0.006	0.832	0.168
68	3RGK	1.4	AT	7215	1326	5888	2869	4346	57	-122	-353	170	0.008	0.043	-0.017	-0.021	0.184	0.816	-0.049	-0.123	0.024	0.039	0.398	0.602
69	3RGK	20.0	AA	4933	1814	3068	4841	91	10	-11	-47	0	0.002	0.006	-0.002	-0.004	0.368	0.622	-0.01	-0.01	0	0.006	0.981	0.019
70	3RGK	20.0	AT	4933	1732	2911	3131	1512	67	-56	-311	19	0.014	0.039	-0.011	-0.019	0.351	0.59	-0.063	-0.099	0.004	0.013	0.635	0.307
71	4ACQ	1.4	AA	240174	45355	194818	182574	53749	82	-489	-1171	322	0	0.002	-0.002	-0.003	0.189	0.811	-0.005	-0.006	0.001	0.006	0.76	0.224
72	4ACQ	1.4	AT	240174	45355	194818	93697	146476	1324	-3835	-12210	9354	0.006	0.029	-0.016	-0.02	0.189	0.811	-0.051	-0.13	0.039	0.064	0.39	0.61
73	4ACQ	20.0	AA	100260	22346	77913	82990	16695	86	-252	-685	116	0.001	0.004	-0.003	-0.003	0.223	0.777	-0.007	-0.008	0.001	0.007	0.828	0.167
74	4ACQ	20.0	AT	100260	21405	71478	51765	41118	525	-1106	-3973	465	0.005	0.025	-0.011	-0.015	0.214	0.713	-0.04	-0.077	0.005	0.011	0.516	0.41
75	4ARX	1.4	AT	85337	19583	65754	45815	39522	341	-1317	1506	-4382	0.0040	0.0174	-0.0154	-0.0200	0.2295	0.7705	0.0176	0.0329	-0.0513	-0.1109	0.5369	0.4631
76	4ARX	20.0	AT	27747	7228	19255	16552	9931	140	-327	-1252	134	0.0050	0.0190	-0.0120	-0.0170	0.2610	0.6940	-0.0450	-0.0760	0.0050	0.0130	0.5970	0.3580
77	4INS	1.4	AA	5265	954	4311	3461	1465	1	-10	-21	7	0	0.002	-0.002	-0.002	0.181	0.819	-0.004	-0.006	0.001	0.005	0.657	0.278
78	4INS	1.4	AT	5265	954	4311	2191	3074	25	-84	-251	118	0.005	0.027	-0.016	-0.02	0.181	0.819	-0.048	-0.115	0.022	0.038	0.416	0.584
79	4INS	20.0	AA	3944	437	2888	2750	1028	0	-7	-18	5	0	0.002	-0.002	-0.003	0.111	0.732	-0.005	-0.007	0.001	0.005	0.697	0.261
80	4INS	20.0	AT	3944	379	2842	1300	1921	8	-38	-91	29	0.002	0.023	-0.01	-0.013	0.096	0.721	-0.023	-0.07	0.008	0.016	0.33	0.487
81	4W8J	1.4	AA	43779	9901	33877	34526	9252	15	-90	-232	58	0	0.002	-0.002	-0.003	0.226	0.774	-0.005	-0.007	0.001	0.006	0.789	0.211
82	4W8J	1.4	AT	43779	9901	33877	19615	24164	248	-711	-2497	1305	0.006	0.025	-0.016	-0.021	0.226	0.774	-0.057	-0.127	0.03	0.054	0.448	0.552
83	4W8J	20.0	AA	27746	7862	19884	24167	3579	19	-71	-197	27	0.001	0.003	-0.003	-0.004	0.283	0.717	-0.007	-0.008	0.001	0.008	0.871	0.129
84	4W8J	20.0	AT	27746	7228	19254	16551	9931	139	-326	-1252	133	0.005	0.019	-0.012	-0.017	0.261	0.694	-0.045	-0.076	0.005	0.013	0.597	0.358
85	6KXS	1.4	AA	136902	28291	108610	110451	24976	47	-292	-676	138	0	0.002	-0.002	-0.003	0.207	0.793	-0.005	-0.006	0.001	0.006	0.807	0.182
86	6KXS	1.4	AT	136902	28291	108610	58733	78168	744	-2207	-7235	4458	0.005	0.026	-0.016	-0.02	0.207	0.793	-0.053	-0.123	0.033	0.057	0.429	0.571
87	6KXS	20.0	AA	66836	14854	51982	60890	5297	33	-190	-457	29	0.001	0.002	-0.003	-0.004	0.222	0.778	-0.007	-0.008	0	0.006	0.911	0.079
88	6KXS	20.0	AT	66836	13663	50559	37792	26429	204	-820	-2731	320	0.003	0.015	-0.012	-0.016	0.204	0.756	-0.041	-0.072	0.005	0.012	0.565	0.395
89	6TAV	1.4	AT	240174	45355	194818	93697	146476	1324	-3835	-12210	9354	0.0055	0.0292	-0.0160	-0.0197	0.1888	0.8112	-0.0508	-0.1303	0.0389	0.0639	0.3901	0.6099
90	6TAV	20.0	AT	100261	21406	71478	51766	12702	525	-1106	-3974	466	0.0052	0.0245	-0.0110	-0.0155	0.2135	0.7129	-0.0396	-0.0768	0.0046	0.0367	0.5163	0.1267

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.

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
11	Cry1Ac protoxin	4ARX	1.4	134.90	151088	26512	26512	85337	85087	307803	0.2583	0.2058	1.0485
12	Cry1Ac protoxin	4ARX	20.0	134.90	151088	435	27312	27747	66424	224437	0.6437	0.5516	3.4694
13	Cytochrome c	1HRC	1.4	12.37	13854	1972	3507	5479	6296	13372	0.4972	0.4586	1.7338
14	Cytochrome c	1HRC	20.0	12.37	13854	121	3853	3973	18590	20381	0.9082	0.6059	1.7298
15	Fibrinogen	1M1J	1.4	311.78	349194	28068	59011	87078	89799	259562	0.2260	0.1687	2.2255
16	Fibrinogen	1M1J	20.0	311.78	349194	895	54598	55493	136825	401292	0.4741	0.4386	4.3282
17	Fibronectin	3M7P	1.4	550.00	616000	1021	1482	2503	3279	4693	0.5417	0.4930	166.5667
18	Fibronectin	3M7P	20.0	550.00	616000	100	2231	2331	15283	7459	0.7919	0.5920	146.8680
19	Glucose oxidase	1GPE	1.4	133.16	149139	11321	25756	37077	36256	147701	0.3645	0.3278	2.6898
20	Glucose oxidase	1GPE	20.0	133.16	149139	319	19857	20175	47646	217450	0.8668	0.6009	3.8104
21	Hemoglobin	1BUW	1.4	64.73	72498	7790	17594	25384	24663	71811	0.3291	0.2879	1.8575
22	Hemoglobin	1BUW	20.0	64.73	72498	232	12471	12703	34847	115622	0.9035	0.6053	2.8427
23	Human (or bovin) Serum Albumin	1BJ5	1.4	67.71	75835	9335	19811	29146	29678	72819	0.2893	0.2418	1.6169
24	Human (or bovin) Serum Albumin	1BJ5	20.0	67.71	75835	387	26596	26983	61309	273000	0.7542	0.5856	1.6224
25	Immunoglobulin G (or anti hPSA)	1IGT	1.4	148.68	166522	19877	39697	59574	63607	169383	0.2485	0.1944	1.6259
26	Immunoglobulin G (or anti hPSA)	1IGT	20.0	148.68	166522	540	36775	37315	82973	322313	0.6092	0.5350	2.9136
27	Immunoglobulin M	2RCJ	1.4	990.00	1108800	137060	175715	312775	422993	253122	0.0619	0.0192	0.8177
28	Immunoglobulin M	2RCJ	20.0	990.00	1108800	2410	165764	168174	336201	1392551	0.3586	0.3213	4.3918
29	Insulin	1HLS	1.4	5.79	6485	1257	1880	3137	4031	6107	0.5150	0.4730	1.4114
30	Insulin	1HLS	20.0	5.79	6485	102	2546	2648	15911	10081	0.8523	0.5994	1.2805
31	Lactoferrin	1B0L	1.4	76.52	85702	8869	19151	28020	28525	88310	0.3423	0.3029	2.0125
32	Lactoferrin	1B0L	20.0	76.52	85702	271	16215	16487	42860	142619	0.8007	0.5932	2.8635
33	Lysozyme	2LYZ	1.4	14.33	16050	2063	3734	5796	6642	16071	0.5313	0.4855	1.8810
34	Lysozyme	2LYZ	20.0	14.33	16050	126	4363	4490	19965	23496	0.8836	0.6028	1.8132
35	Myoglobin	3RGK	1.4	17.98	20138	2497	4719	7216	7993	19109	0.4790	0.4430	1.9188
36	Myoglobin	3RGK	20.0	17.98	20138	138	5040	5178	21387	28331	0.8680	0.6011	2.0024

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

Additional Information

For access to the ProMS source code, please contact the lab
- User manual can be downloaded here

Relevant papers & links:

- Nicolau’s paper on mapping hydrophobicity on molecular surfaces at the atomic level
- Nicolau’s paper on ProMS’ predecessor, PSPC
- Connolly’s algorithm to compute molecular surfaces analytically
- Connolly’s molecular surface package
- Schrodinger’s PyMOL