PyMACS dashboard

RAT apo-vs-ligand comparison

PyMACS molecular-dynamics dashboard summarizing global protein behavior, local flexibility, ligand pose stability, contact persistence, and ligand-to-ligand differences.

Runs: 3Ligand-bound: 2Apo/reference: RAT_APOMode: Fast

GitHub: PyMACS Paper Contact Authors

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Overview

At-a-glance summary

Runs compared

2 ligand-bound + apo/reference

Apo reference

RAT_APO

Baseline protein state

Mean protein RMSD

3.457

Å, across available runs

Mean Rg

20.677

Å, compactness signal

Mean ligand RMSD

1.880

Å, ligand pose stability

Contact residues tracked

From summary files unless --use-framewise

Binding-site summaries

Contact residue RMSF vs apo

Pairwise ligand comparisons

Ligand-vs-ligand table rows

Reading guide

How to read this dashboard

Use the panels as a linked set of molecular-dynamics readouts: global protein motion, local residue flexibility, ligand pose stability, and contact persistence are most informative when interpreted together.

Global protein state

RMSD tracks overall conformational drift, Rg tracks compactness, and RMSF identifies flexible or stabilized residue regions.

Ligand behavior

Ligand RMSD is strongest when interpreted with contact persistence. A stable pose should retain meaningful residue contacts over time.

Contact fingerprints

The contact heatmap includes ligand-bound systems only and summarizes which pocket residues are repeatedly contacted.

Fast mode uses existing summary files and skips large framewise contact tables unless --use-framewise is requested.

Analysis scope

This dashboard compares the apo/reference protein state with ligand-bound simulations using global dynamics, local residue flexibility, and ligand-contact behavior.

In the protein RMSF plot, each ligand includes a hidden-by-default interacting-residue guide trace. Toggle those traces from the legend to connect flexibility changes with contacting residues.

Data exports

Interactive figures are shown in the HTML. Core numeric tables are exported under data/RAT, including summary metrics, apo-relative deltas, contact matrices, and ligand comparison tables.

Ligand identity

Ligand structures

Visual identity and embedded 3D geometry checks for each ligand-bound simulation.

Balovaptan

RAT_BALO

Formula C22H24ClN5O+MW 409.92

3D viewdrag · zoom

Chemical identifier

CN1Cc2cc(Cl)ccc2-n2c(nnc2[C@H]2CC[C@H](Oc3ccccn3)CC2)C1

UMF-504

RAT_UMF

Formula C23H23ClN6O3+MW 466.93

3D viewdrag · zoom

Chemical identifier

NC(=O)C(=O)N1Cc2cc(Cl)ccc2-n2c(nnc2[C@H]2CC[C@H](Oc3ccccn3)CC2)C1

protein panels

Protein-state figures

Hover over the circular i icon on each graph for interpretation notes and expected trends.

Interactive figure

Protein RMSD overlay

What it means: RMSD measures how far the protein conformation has moved from the starting/reference structure.

Expected trend: A stable simulation usually rises early, then plateaus. A ligand-bound trace lower than apo can suggest global stabilization; higher or continuously rising traces may indicate larger rearrangement or incomplete equilibration.

How to read it: Compare plateau height, late-time drift, and whether ligand-bound runs separate from apo. Use this as a global signal, not as direct binding proof.

Global protein structural drift over time for apo/reference and ligand-bound runs.

Interactive figure

Radius of gyration overlay

What it means: Rg summarizes how spread out the protein mass is around its center of mass.

Expected trend: Flat Rg suggests stable compactness. A ligand that lowers Rg versus apo may compact the protein; a higher Rg may indicate expansion/opening.

How to read it: Interpret with RMSD/RMSF: Rg changes tell you compactness, not necessarily whether the pose is good.

Protein compactness over time. Lower Rg generally means a more compact protein state.

Interactive figure

Protein RMSF overlay

What it means: RMSF measures how much each residue fluctuates across the trajectory.

Expected trend: Ligand-stabilized local regions often show reduced RMSF near contact residues. Flexible loops/termini naturally show peaks.

How to read it: Focus on contact-adjacent regions and ligand-specific peak changes. Toggle guide traces to see where contacts occur.

Per-residue flexibility profile, with optional interacting-residue guide traces in the legend.

Interactive figure

Apo-relative global protein deltas

What it means: Positive bars mean the ligand-bound run is higher than apo; negative bars mean lower than apo.

Expected trend: Negative RMSD/RMSF can imply stabilization; negative Rg suggests compaction. Large positive values may reflect opening, flexibility gain, or drift.

How to read it: This is a compact view of how each ligand shifts the global protein state.

Ligand-bound global metrics minus the apo/reference metric.

Interactive figure

Ligand-contact residue RMSF deltas vs apo

What it means: Each point/bar is bound-state RMSF minus apo RMSF for a ligand-contacting residue.

Expected trend: Negative deltas indicate contact residues became more rigid/stabilized; positive deltas indicate they became more flexible.

How to read it: Prioritize high-contact residues with consistent negative deltas when arguing local stabilization.

Local flexibility change at residues contacted by ligand, relative to apo.

ligand panels

Ligand-behavior figures

Hover over the circular i icon on each graph for interpretation notes and expected trends.

Interactive figure

Ligand RMSD overlay

What it means: Ligand RMSD tracks how much the ligand changes position/conformation relative to its starting pose.

Expected trend: A stable binder often has low-to-moderate RMSD and a plateau. Large final RMSD or monotonic increase can flag pose drift or possible dissociation.

How to read it: Use together with contact persistence. A ligand can move internally while maintaining key contacts.

Ligand pose movement over time for bound simulations.

Interactive figure

Ligand-contact residue summary heatmap

What it means: Color intensity is the fraction of frames in which a residue contacted the ligand.

Expected trend: Persistent contacts appear warm/high. Ligands with different binding modes show different residue fingerprints.

How to read it: Rows are ligand-bound runs; columns are top contact residues. Use this as a pocket fingerprint, not a direct affinity score.

Ligand-only contact fraction matrix. APO is intentionally excluded because it has no ligand-contact profile.

Interactive figure

Interaction type composition

What it means: Shows whether interactions are mostly hydrophobic, polar, hydrogen bonding, ionic, water-mediated, or van der Waals-like.

Expected trend: Better-behaved poses often preserve a coherent interaction signature instead of collapsing to nonspecific weak contacts.

How to read it: Compare composition across ligands to explain why two ligands with similar RMSD may behave differently.

Fractional makeup of contact/interaction categories by run.

compare panels

Ligand comparison figures

Hover over the circular i icon on each graph for interpretation notes and expected trends.

Interactive figure

Ligand behavior vs protein-state behavior

What it means: Each point is a ligand-bound run. Position shows ligand movement and protein movement; marker size reflects contact-residue count; color reflects Rg.

Expected trend: Promising stable systems often cluster toward lower ligand RMSD and lower/plateaued protein RMSD, with meaningful contact persistence.

How to read it: Use as a triage plot to select systems worth deeper structural inspection.

Compact ligand-vs-protein behavior map using ligand RMSD, protein RMSD, contacts, and Rg.

Interactive figure

Contact-profile similarity

What it means: High similarity means two ligands contacted a similar residue set with similar frequencies.

Expected trend: Ligands sharing a binding mode should cluster high; divergent binding modes should be lower.

How to read it: Useful for grouping ligands by pocket behavior before selecting representative cases.

Ligand-vs-ligand cosine similarity based on residue contact fingerprints.

Interactive figure

Interaction-type similarity

What it means: High similarity means two ligands rely on similar classes of interactions.

Expected trend: Similar scaffolds or poses may share interaction signatures; outliers may reveal different binding chemistry.

How to read it: Pair with contact-profile similarity to separate same-pocket/different-chemistry cases from different-pocket cases.

Ligand-vs-ligand similarity based on interaction type composition.

Data tables

Summary metrics

Run	family	state	is_apo	ligand_display	protein_rmsd_mean_A	protein_rmsd_last_half_mean_A	protein_rmsd_final_A	protein_rmsd_slope_A_per_ns	protein_rmsf_mean_A	protein_rmsf_std_A	rg_mean_A	rg_last_half_mean_A	rg_final_A	rg_slope_A_per_ns	ligand_rmsd_mean_A	ligand_rmsd_last_half_mean_A	ligand_rmsd_final_A	ligand_rmsd_slope_A_per_ns	unique_contact_residues	used_framewise	framewise_file_size_mb	has_protein_rmsd	has_protein_rmsf	has_rg	has_ligand_rmsd	has_residue_contacts	has_interaction_types	has_ligand_visual	protein_rmsd_std_A	rg_std_A	ligand_rmsd_std_A	has_ligand_rmsf
RAT_APO	RAT	APO	True	APO	3.4934	3.9156	3.6535	0.0036	1.5702	1.2261	20.6735	20.6748	20.6656	0.0002					0	False		True	True	True	False	False	False	False	0.5942	0.1335		False
RAT_BALO	RAT	BALO	False	Balovaptan	3.0977	3.4946	3.7527	0.0032	1.5487	1.1153	20.6903	20.7312	20.6005	0.0004	1.6643	1.7420	1.6890	0.0007	34	False	73.5952	True	True	True	True	True	True	True	0.5333	0.1434	0.1538	False
RAT_UMF	RAT	UMF	False	UMF-504	3.7789	4.0581	3.9296	0.0027	1.7353	1.2711	20.6677	20.6040	20.5655	-0.0004	2.0947	2.2522	2.4628	0.0014	32	False	65.0482	True	True	True	True	True	True	True	0.6537	0.1262	0.3684	False

Data availability

Run	State	Ligand	Protein RMSD	Protein RMSF	Rg	Ligand RMSD	Ligand RMSF	Residue contact summary	Interaction type summary	2D ligand	Ligand file	Framewise used	Framewise MB
RAT_APO	APO	APO	Yes	Yes	Yes	No	No	No	No	No		No
RAT_BALO	BALO	Balovaptan	Yes	Yes	Yes	Yes	No	Yes	Yes	Yes	UNL.cgenff.mol2	No	73.6
RAT_UMF	UMF	UMF-504	Yes	Yes	Yes	Yes	No	Yes	Yes	Yes	UNL.cgenff.mol2	No	65.0

Apo-relative global protein deltas

Run	Ligand	ApoRun	protein_rmsd_mean_A_apo	protein_rmsd_mean_A_bound	delta_protein_rmsd_mean_A	protein_rmsd_last_half_mean_A_apo	protein_rmsd_last_half_mean_A_bound	delta_protein_rmsd_last_half_mean_A	protein_rmsd_final_A_apo	protein_rmsd_final_A_bound	delta_protein_rmsd_final_A	protein_rmsf_mean_A_apo	protein_rmsf_mean_A_bound	delta_protein_rmsf_mean_A	rg_mean_A_apo	rg_mean_A_bound	delta_rg_mean_A	rg_last_half_mean_A_apo	rg_last_half_mean_A_bound	delta_rg_last_half_mean_A	rg_final_A_apo	rg_final_A_bound	delta_rg_final_A	protein_rmsd_slope_A_per_ns_apo	protein_rmsd_slope_A_per_ns_bound	delta_protein_rmsd_slope_A_per_ns	rg_slope_A_per_ns_apo	rg_slope_A_per_ns_bound	delta_rg_slope_A_per_ns	protein_state_call
RAT_BALO	Balovaptan	RAT_APO	3.4934	3.0977	-0.3957	3.9156	3.4946	-0.4210	3.6535	3.7527	0.0991	1.5702	1.5487	-0.0215	20.6735	20.6903	0.0168	20.6748	20.7312	0.0564	20.6656	20.6005	-0.0651	0.0036	0.0032	-0.0004	0.0002	0.0004	0.0002	similar compactness; lower global RMSD
RAT_UMF	UMF-504	RAT_APO	3.4934	3.7789	0.2855	3.9156	4.0581	0.1426	3.6535	3.9296	0.2761	1.5702	1.7353	0.1651	20.6735	20.6677	-0.0058	20.6748	20.6040	-0.0708	20.6656	20.5655	-0.1002	0.0036	0.0027	-0.0009	0.0002	-0.0004	-0.0006	similar compactness; similar global RMSD; globally more flexible

Binding-site RMSF summary

Run	Ligand	MatchedContactResidues	Mean_BindingSite_Delta_RMSF_A	Weighted_BindingSite_Delta_RMSF_A	MeanAbs_BindingSite_Delta_RMSF_A	RigidifiedResidues_N	MoreFlexibleResidues_N	BindingSiteCall
RAT_BALO	Balovaptan	34	-0.0162	-0.0309	0.2698	19	15	binding site similar to apo
RAT_UMF	UMF-504	32	0.0937	0.1078	0.3457	10	22	binding site loosened/more flexible

Ligand-contact residue RMSF deltas vs apo

Run	Ligand	Residue	ResidueKey	ResNum	ContactFraction	ContactCount	Apo_RMSF_A	Bound_RMSF_A	Delta_RMSF_A	Direction	Abs_Delta_RMSF_A
RAT_BALO	Balovaptan	GLU5454	54	54	0.1161	11.6058	1.6623	2.7164	1.0541	loosened / more flexible	1.0541
RAT_BALO	Balovaptan	LEU5858	58	58	0.1278	12.7757	1.2734	1.7036	0.4302	loosened / more flexible	0.4302
RAT_BALO	Balovaptan	PHE103103	103	103	0.1435	14.3497	1.1386	1.3567	0.2182	loosened / more flexible	0.2182
RAT_BALO	Balovaptan	GLN104104	104	104	0.9999	99.9900	1.2510	1.3790	0.1280	loosened / more flexible	0.1280
RAT_BALO	Balovaptan	VAL105105	105	105	0.1074	10.7398	1.0128	1.2375	0.2247	loosened / more flexible	0.2247
RAT_BALO	Balovaptan	PRO107107	107	107	0.6662	66.6187	1.3042	1.5675	0.2633	loosened / more flexible	0.2633
RAT_BALO	Balovaptan	GLN108108	108	108	0.9619	96.1881	1.3546	1.6898	0.3353	loosened / more flexible	0.3353
RAT_BALO	Balovaptan	LYS128128	128	128	0.9736	97.3561	0.6926	0.8763	0.1837	loosened / more flexible	0.1837
RAT_BALO	Balovaptan	GLN131131	131	131	1.0000	99.9980	0.7557	0.9176	0.1619	loosened / more flexible	0.1619
RAT_BALO	Balovaptan	VAL132132	132	132	0.9995	99.9480	0.7345	0.8072	0.0728	loosened / more flexible	0.0728
RAT_BALO	Balovaptan	MET135135	135	135	0.9973	99.7300	0.6614	0.7815	0.1201	loosened / more flexible	0.1201
RAT_BALO	Balovaptan	GLN185185	185	185	0.9995	99.9540	1.4072	0.8899	-0.5173	stabilized / rigidified	0.5173
RAT_BALO	Balovaptan	ILE188188	188	188	0.6219	62.1868	1.2994	1.1029	-0.1965	stabilized / rigidified	0.1965
RAT_BALO	Balovaptan	PHE189189	189	189	0.9927	99.2680	1.0129	0.9998	-0.0131	stabilized / rigidified	0.0131
RAT_BALO	Balovaptan	ALA207207	207	207	0.2973	29.7254	1.3363	1.2410	-0.0954	stabilized / rigidified	0.0954
RAT_BALO	Balovaptan	PHE209209	209	209	0.9752	97.5180	1.4321	1.3197	-0.1123	stabilized / rigidified	0.1123
RAT_BALO	Balovaptan	THR215215	215	215	0.5321	53.2089	1.4698	1.0722	-0.3976	stabilized / rigidified	0.3976
RAT_BALO	Balovaptan	TYR218218	218	218	0.9999	99.9920	1.1848	0.9558	-0.2290	stabilized / rigidified	0.2290
RAT_BALO	Balovaptan	VAL219219	219	219	1.0000	100.0000	1.0184	0.8458	-0.1726	stabilized / rigidified	0.1726
RAT_BALO	Balovaptan	MET222222	222	222	0.9977	99.7700	0.9988	0.8529	-0.1459	stabilized / rigidified	0.1459
RAT_BALO	Balovaptan	THR223223	223	223	0.9995	99.9460	0.9156	0.8144	-0.1012	stabilized / rigidified	0.1012
RAT_BALO	Balovaptan	VAL226226	226	226	0.9437	94.3661	1.0849	0.7894	-0.2955	stabilized / rigidified	0.2955
RAT_BALO	Balovaptan	PHE227227	227	227	0.1352	13.5217	1.0017	0.8472	-0.1545	stabilized / rigidified	0.1545
RAT_BALO	Balovaptan	TRP310310	310	310	0.1610	16.0957	1.0545	0.7997	-0.2548	stabilized / rigidified	0.2548
RAT_BALO	Balovaptan	PHE313313	313	313	0.9996	99.9560	0.9287	0.8928	-0.0360	stabilized / rigidified	0.0360
RAT_BALO	Balovaptan	PHE314314	314	314	0.9942	99.4180	0.8867	0.9826	0.0958	loosened / more flexible	0.0958
RAT_BALO	Balovaptan	GLN317317	317	317	0.9993	99.9280	1.0331	1.0351	0.0020	loosened / more flexible	0.0020
RAT_BALO	Balovaptan	MET318318	318	318	0.3360	33.5993	1.1358	1.1309	-0.0050	stabilized / rigidified	0.0050
RAT_BALO	Balovaptan	GLU332332	332	332	0.3505	35.0453	5.6443	4.3041	-1.3402	stabilized / rigidified	1.3402
RAT_BALO	Balovaptan	ILE336336	336	336	0.7519	75.1905	1.3893	1.8132	0.4239	loosened / more flexible	0.4239
RAT_BALO	Balovaptan	THR337337	337	337	0.8444	84.4363	1.4566	2.0530	0.5963	loosened / more flexible	0.5963
RAT_BALO	Balovaptan	ALA340340	340	340	0.9999	99.9900	1.2757	1.1829	-0.0928	stabilized / rigidified	0.0928
RAT_BALO	Balovaptan	LEU341341	341	341	0.8802	88.0202	1.5975	1.3603	-0.2372	stabilized / rigidified	0.2372
RAT_BALO	Balovaptan	SER344344	344	344	0.5742	57.4229	1.3678	0.9019	-0.4659	stabilized / rigidified	0.4659
RAT_UMF	UMF-504	GLU5454	54	54	0.2037	20.3736	1.6623	1.9297	0.2674	loosened / more flexible	0.2674
RAT_UMF	UMF-504	LEU5858	58	58	0.9581	95.8101	1.2734	1.5996	0.3262	loosened / more flexible	0.3262
RAT_UMF	UMF-504	ILE6161	61	61	0.5793	57.9268	1.3307	1.5720	0.2414	loosened / more flexible	0.2414
RAT_UMF	UMF-504	GLN104104	104	104	0.9970	99.7020	1.2510	1.8460	0.5950	loosened / more flexible	0.5950
RAT_UMF	UMF-504	VAL105105	105	105	0.7087	70.8686	1.0128	1.5471	0.5343	loosened / more flexible	0.5343
RAT_UMF	UMF-504	GLN108108	108	108	0.9638	96.3761	1.3546	1.9266	0.5720	loosened / more flexible	0.5720
RAT_UMF	UMF-504	TYR115115	115	115	0.6814	68.1386	3.0282	3.4898	0.4616	loosened / more flexible	0.4616
RAT_UMF	UMF-504	ARG116116	116	116	0.2234	22.3376	2.2415	2.8605	0.6190	loosened / more flexible	0.6190
RAT_UMF	UMF-504	LYS128128	128	128	0.3199	31.9914	0.6926	0.9666	0.2740	loosened / more flexible	0.2740
RAT_UMF	UMF-504	GLN131131	131	131	0.3266	32.6593	0.7557	0.9773	0.2216	loosened / more flexible	0.2216
RAT_UMF	UMF-504	MET135135	135	135	0.7311	73.1125	0.6614	0.6455	-0.0159	stabilized / rigidified	0.0159
RAT_UMF	UMF-504	ILE188188	188	188	0.2644	26.4355	1.2994	1.3675	0.0681	loosened / more flexible	0.0681
RAT_UMF	UMF-504	PHE189189	189	189	0.6495	64.9547	1.0129	1.2712	0.2582	loosened / more flexible	0.2582
RAT_UMF	UMF-504	ALA207207	207	207	0.6626	66.2647	1.3363	1.4835	0.1472	loosened / more flexible	0.1472
RAT_UMF	UMF-504	PHE209209	209	209	0.9271	92.7121	1.4321	1.5609	0.1289	loosened / more flexible	0.1289
RAT_UMF	UMF-504	GLN211211	211	211	0.1701	17.0077	2.7479	2.7734	0.0255	loosened / more flexible	0.0255
RAT_UMF	UMF-504	THR215215	215	215	0.9307	93.0681	1.4698	1.0910	-0.3788	stabilized / rigidified	0.3788
RAT_UMF	UMF-504	TYR218218	218	218	0.9936	99.3620	1.1848	0.7990	-0.3858	stabilized / rigidified	0.3858
RAT_UMF	UMF-504	VAL219219	219	219	0.9995	99.9520	1.0184	0.7996	-0.2187	stabilized / rigidified	0.2187
RAT_UMF	UMF-504	MET222222	222	222	0.9995	99.9480	0.9988	0.6497	-0.3490	stabilized / rigidified	0.3490
RAT_UMF	UMF-504	THR223223	223	223	0.4792	47.9150	0.9156	0.6653	-0.2503	stabilized / rigidified	0.2503
RAT_UMF	UMF-504	PHE313313	313	313	0.9992	99.9220	0.9287	0.8584	-0.0704	stabilized / rigidified	0.0704
RAT_UMF	UMF-504	PHE314314	314	314	0.9925	99.2460	0.8867	0.8508	-0.0360	stabilized / rigidified	0.0360
RAT_UMF	UMF-504	GLN317317	317	317	0.9998	99.9800	1.0331	1.1904	0.1572	loosened / more flexible	0.1572
RAT_UMF	UMF-504	SER320320	320	320	0.1461	14.6137	1.4044	1.6554	0.2510	loosened / more flexible	0.2510
RAT_UMF	UMF-504	VAL321321	321	321	0.4916	49.1570	1.6187	1.7985	0.1798	loosened / more flexible	0.1798
RAT_UMF	UMF-504	SER331331	331	331	0.2185	21.8476	6.4630	4.3929	-2.0701	stabilized / rigidified	2.0701
RAT_UMF	UMF-504	ILE336336	336	336	0.5244	52.4430	1.3893	2.0896	0.7003	loosened / more flexible	0.7003
RAT_UMF	UMF-504	THR337337	337	337	0.8374	83.7423	1.4566	1.5173	0.0607	loosened / more flexible	0.0607
RAT_UMF	UMF-504	ALA340340	340	340	0.9540	95.3981	1.2757	1.5928	0.3172	loosened / more flexible	0.3172
RAT_UMF	UMF-504	LEU341341	341	341	0.9580	95.8001	1.5975	1.3404	-0.2572	stabilized / rigidified	0.2572
RAT_UMF	UMF-504	SER344344	344	344	0.8510	85.1003	1.3678	1.9922	0.6244	loosened / more flexible	0.6244

Ligand-vs-ligand comparison

Ligand_A_Run	Ligand_A	Ligand_B_Run	Ligand_B	ContactResidue_Jaccard	SharedContactResidues_N	UniqueContactResidues_A_N	UniqueContactResidues_B_N	InteractionType_CosineSimilarity	Delta_ProteinRMSDMean_A_minus_B	Delta_RgMean_A_minus_B	Delta_LigandRMSDMean_A_minus_B
RAT_BALO	Balovaptan	RAT_UMF	UMF-504	0.6098	25	9	7	0.9998	-0.6812	0.0226	-0.4304

Ligand stability flags

Run	Ligand	OverallCall	ProteinStateCall	BindingSiteCall	PossibleDissociation	FlagReasons	LigandRMSDMean_A	LigandRMSDFinal_A	InteractionLoadRatio_LastOverFirst
RAT_BALO	Balovaptan	no obvious instability flag	similar compactness; lower global RMSD	binding site similar to apo	False		1.6643	1.6890
RAT_UMF	UMF-504	binding-site flexibility increaser	similar compactness; similar global RMSD; globally more flexible	binding site loosened/more flexible	False		2.0947	2.4628

Run details

RAT_APO — state=APO — ligand=APO

Metrics

Metric	Value
family	RAT
state	APO
is_apo	True
ligand_display	APO
protein_rmsd_mean_A	3.4934
protein_rmsd_std_A	0.5942
protein_rmsd_final_A	3.6535
protein_rmsd_last_half_mean_A	3.9156
protein_rmsd_slope_A_per_ns	0.0036
protein_rmsf_mean_A	1.5702
protein_rmsf_std_A	1.2261
rg_mean_A	20.6735
rg_std_A	0.1335
rg_final_A	20.6656
rg_last_half_mean_A	20.6748
rg_slope_A_per_ns	0.0002
ligand_rmsd_mean_A
ligand_rmsd_std_A
ligand_rmsd_final_A
ligand_rmsd_last_half_mean_A
ligand_rmsd_slope_A_per_ns
ligand_rmsf_mean_A
bound_complex_rmsd_mean_A
has_protein_rmsd	True
has_protein_rmsf	True
has_rg	True
has_ligand_rmsd	False
has_ligand_rmsf	False
has_residue_contacts	False
has_interaction_types	False
has_ligand_visual	False
interaction_rows
unique_contact_residues	0
interaction_frame_count
interaction_load_first_half
interaction_load_last_half
interaction_load_ratio_last_over_first
used_framewise	False
framewise_file_size_mb

Detected files

{
  "protein_rmsd_csv": "/home/jxs794/MD_JOBS/Nahuel/RAT_APO/Analysis_Results/Protein_RMSD.csv",
  "protein_rmsf_csvs": "/home/jxs794/MD_JOBS/Nahuel/RAT_APO/Analysis_Results/RMSF_V1AR_Rat.csv;/home/jxs794/MD_JOBS/Nahuel/RAT_APO/Analysis_Results/RMSF_V1AR_Rat_per_residue.csv",
  "radius_gyration_csv": "/home/jxs794/MD_JOBS/Nahuel/RAT_APO/Analysis_Results/Radius_of_Gyration_Protein.csv",
  "ligand_rmsd_csv": null,
  "ligand_rmsf_csv": null,
  "bound_complex_rmsd_csv": null,
  "residue_summary_csv": null,
  "interaction_type_summary_csv": null,
  "framewise_interaction_csv_skipped_by_default": null,
  "contact_hover_framewise_csv": null,
  "interaction_type_framewise_csv": null,
  "ligand_structure_file": null
}

RAT_BALO — state=BALO — ligand=Balovaptan

Metrics

Metric	Value
family	RAT
state	BALO
is_apo	False
ligand_display	Balovaptan
protein_rmsd_mean_A	3.0977
protein_rmsd_std_A	0.5333
protein_rmsd_final_A	3.7527
protein_rmsd_last_half_mean_A	3.4946
protein_rmsd_slope_A_per_ns	0.0032
protein_rmsf_mean_A	1.5487
protein_rmsf_std_A	1.1153
rg_mean_A	20.6903
rg_std_A	0.1434
rg_final_A	20.6005
rg_last_half_mean_A	20.7312
rg_slope_A_per_ns	0.0004
ligand_rmsd_mean_A	1.6643
ligand_rmsd_std_A	0.1538
ligand_rmsd_final_A	1.6890
ligand_rmsd_last_half_mean_A	1.7420
ligand_rmsd_slope_A_per_ns	0.0007
ligand_rmsf_mean_A
bound_complex_rmsd_mean_A
has_protein_rmsd	True
has_protein_rmsf	True
has_rg	True
has_ligand_rmsd	True
has_ligand_rmsf	False
has_residue_contacts	True
has_interaction_types	True
has_ligand_visual	True
interaction_rows
unique_contact_residues	34
interaction_frame_count
interaction_load_first_half
interaction_load_last_half
interaction_load_ratio_last_over_first
used_framewise	False
framewise_file_size_mb	73.5952

Detected files

{
  "protein_rmsd_csv": "/home/jxs794/MD_JOBS/Nahuel/RAT_BALO/Analysis_Results/Protein_RMSD.csv",
  "protein_rmsf_csvs": "/home/jxs794/MD_JOBS/Nahuel/RAT_BALO/Analysis_Results/RMSF_V1AR_Rat.csv;/home/jxs794/MD_JOBS/Nahuel/RAT_BALO/Analysis_Results/RMSF_V1AR_Rat_per_residue.csv",
  "radius_gyration_csv": "/home/jxs794/MD_JOBS/Nahuel/RAT_BALO/Analysis_Results/Radius_of_Gyration_Protein_Ligand_Complex.csv",
  "ligand_rmsd_csv": "/home/jxs794/MD_JOBS/Nahuel/RAT_BALO/Analysis_Results/Balovaptan_Ligand_RMSD.csv",
  "ligand_rmsf_csv": "/home/jxs794/MD_JOBS/Nahuel/RAT_BALO/Analysis_Results/Balovaptan_Ligand_RMSF.csv",
  "bound_complex_rmsd_csv": null,
  "residue_summary_csv": "/home/jxs794/MD_JOBS/Nahuel/RAT_BALO/Analysis_Results/UNL_contact_frequency_filtered.csv",
  "interaction_type_summary_csv": "/home/jxs794/MD_JOBS/Nahuel/RAT_BALO/Analysis_Results/InteractionTypes_Summary.csv",
  "framewise_interaction_csv_skipped_by_default": "/home/jxs794/MD_JOBS/Nahuel/RAT_BALO/Analysis_Results/FilteredContacts_Framewise.csv",
  "contact_hover_framewise_csv": "/home/jxs794/MD_JOBS/Nahuel/RAT_BALO/Analysis_Results/FilteredContacts_Framewise.csv",
  "interaction_type_framewise_csv": "/home/jxs794/MD_JOBS/Nahuel/RAT_BALO/Analysis_Results/InteractionTypes_Framewise.csv",
  "ligand_structure_file": "/home/jxs794/MD_JOBS/Nahuel/RAT_BALO/UNL.cgenff.mol2"
}

RAT_UMF — state=UMF — ligand=UMF-504

Metrics

Metric	Value
family	RAT
state	UMF
is_apo	False
ligand_display	UMF-504
protein_rmsd_mean_A	3.7789
protein_rmsd_std_A	0.6537
protein_rmsd_final_A	3.9296
protein_rmsd_last_half_mean_A	4.0581
protein_rmsd_slope_A_per_ns	0.0027
protein_rmsf_mean_A	1.7353
protein_rmsf_std_A	1.2711
rg_mean_A	20.6677
rg_std_A	0.1262
rg_final_A	20.5655
rg_last_half_mean_A	20.6040
rg_slope_A_per_ns	-0.0004
ligand_rmsd_mean_A	2.0947
ligand_rmsd_std_A	0.3684
ligand_rmsd_final_A	2.4628
ligand_rmsd_last_half_mean_A	2.2522
ligand_rmsd_slope_A_per_ns	0.0014
ligand_rmsf_mean_A
bound_complex_rmsd_mean_A
has_protein_rmsd	True
has_protein_rmsf	True
has_rg	True
has_ligand_rmsd	True
has_ligand_rmsf	False
has_residue_contacts	True
has_interaction_types	True
has_ligand_visual	True
interaction_rows
unique_contact_residues	32
interaction_frame_count
interaction_load_first_half
interaction_load_last_half
interaction_load_ratio_last_over_first
used_framewise	False
framewise_file_size_mb	65.0482

Detected files

{
  "protein_rmsd_csv": "/home/jxs794/MD_JOBS/Nahuel/RAT_UMF/Analysis_Results/Protein_RMSD.csv",
  "protein_rmsf_csvs": "/home/jxs794/MD_JOBS/Nahuel/RAT_UMF/Analysis_Results/RMSF_V1AR_Rat.csv;/home/jxs794/MD_JOBS/Nahuel/RAT_UMF/Analysis_Results/RMSF_V1AR_Rat_per_residue.csv",
  "radius_gyration_csv": "/home/jxs794/MD_JOBS/Nahuel/RAT_UMF/Analysis_Results/Radius_of_Gyration_Protein_Ligand_Complex.csv",
  "ligand_rmsd_csv": "/home/jxs794/MD_JOBS/Nahuel/RAT_UMF/Analysis_Results/UMF-504_Ligand_RMSD.csv",
  "ligand_rmsf_csv": "/home/jxs794/MD_JOBS/Nahuel/RAT_UMF/Analysis_Results/UMF-504_Ligand_RMSF.csv",
  "bound_complex_rmsd_csv": null,
  "residue_summary_csv": "/home/jxs794/MD_JOBS/Nahuel/RAT_UMF/Analysis_Results/UNL_contact_frequency_filtered.csv",
  "interaction_type_summary_csv": "/home/jxs794/MD_JOBS/Nahuel/RAT_UMF/Analysis_Results/InteractionTypes_Summary.csv",
  "framewise_interaction_csv_skipped_by_default": "/home/jxs794/MD_JOBS/Nahuel/RAT_UMF/Analysis_Results/FilteredContacts_Framewise.csv",
  "contact_hover_framewise_csv": "/home/jxs794/MD_JOBS/Nahuel/RAT_UMF/Analysis_Results/FilteredContacts_Framewise.csv",
  "interaction_type_framewise_csv": "/home/jxs794/MD_JOBS/Nahuel/RAT_UMF/Analysis_Results/InteractionTypes_Framewise.csv",
  "ligand_structure_file": "/home/jxs794/MD_JOBS/Nahuel/RAT_UMF/UNL.cgenff.mol2"
}