PyMACS dashboard

MOUSE 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: MOUSE_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

MOUSE_APO

Baseline protein state

Mean protein RMSD

3.070

Å, across available runs

Mean Rg

20.378

Å, compactness signal

Mean ligand RMSD

1.589

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/MOUSE, 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

MOUSE_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

MOUSE_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
MOUSE_APO	MOUSE	APO	True	APO	3.7454	3.9183	3.5791	0.0019	1.3588	1.3061	20.4762	20.5074	20.3275	0.0000					0	False		True	True	True	False	False	False	False	0.4606	0.1301		False
MOUSE_BALO	MOUSE	BALO	False	Balovaptan	2.6260	2.8388	2.9260	0.0018	18.3545	6.3912	20.3311	20.3193	20.3337	-0.0002	1.4673	1.4933	1.4041	0.0002	29	False	67.3507	True	True	True	True	True	True	True	0.3048	0.1078	0.1314	False
MOUSE_UMF	MOUSE	UMF	False	UMF-504	2.8388	2.9946	3.2097	0.0013	1.3780	0.9728	20.3279	20.2844	20.3769	-0.0003	1.7108	1.7261	1.7722	0.0000	29	False	71.0017	True	True	True	True	True	True	True	0.2595	0.1386	0.1260	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
MOUSE_APO	APO	APO	Yes	Yes	Yes	No	No	No	No	No		No
MOUSE_BALO	BALO	Balovaptan	Yes	Yes	Yes	Yes	No	Yes	Yes	Yes	UNL.cgenff.mol2	No	67.4
MOUSE_UMF	UMF	UMF-504	Yes	Yes	Yes	Yes	No	Yes	Yes	Yes	UNL.cgenff.mol2	No	71.0

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
MOUSE_BALO	Balovaptan	MOUSE_APO	3.7454	2.6260	-1.1193	3.9183	2.8388	-1.0794	3.5791	2.9260	-0.6531	1.3588	18.3545	16.9957	20.4762	20.3311	-0.1451	20.5074	20.3193	-0.1881	20.3275	20.3337	0.0063	0.0019	0.0018	-0.0001	0.0000	-0.0002	-0.0002	similar compactness; lower global RMSD; globally more flexible
MOUSE_UMF	UMF-504	MOUSE_APO	3.7454	2.8388	-0.9065	3.9183	2.9946	-0.9237	3.5791	3.2097	-0.3694	1.3588	1.3780	0.0192	20.4762	20.3279	-0.1483	20.5074	20.2844	-0.2230	20.3275	20.3769	0.0495	0.0019	0.0013	-0.0006	0.0000	-0.0003	-0.0003	more compact; lower global RMSD

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
MOUSE_BALO	Balovaptan	29	13.9183	13.4134	13.9183	0	29	binding site loosened/more flexible
MOUSE_UMF	UMF-504	29	0.1380	0.1157	0.1830	6	23	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
MOUSE_BALO	Balovaptan	GLU5454	54	54	0.8891	88.9082	1.3364	17.7016	16.3651	loosened / more flexible	16.3651
MOUSE_BALO	Balovaptan	LEU5858	58	58	0.9909	99.0920	0.8269	14.9193	14.0923	loosened / more flexible	14.0923
MOUSE_BALO	Balovaptan	GLN104104	104	104	1.0000	99.9980	0.7102	10.4128	9.7026	loosened / more flexible	9.7026
MOUSE_BALO	Balovaptan	GLN108108	108	108	1.0000	99.9960	0.8683	14.6699	13.8016	loosened / more flexible	13.8016
MOUSE_BALO	Balovaptan	LYS128128	128	128	0.9479	94.7861	0.5821	14.9706	14.3885	loosened / more flexible	14.3885
MOUSE_BALO	Balovaptan	GLN131131	131	131	0.9998	99.9780	0.6261	10.7377	10.1117	loosened / more flexible	10.1117
MOUSE_BALO	Balovaptan	VAL132132	132	132	0.4218	42.1812	0.6157	9.4787	8.8630	loosened / more flexible	8.8630
MOUSE_BALO	Balovaptan	MET135135	135	135	0.9887	98.8740	0.6196	4.9830	4.3634	loosened / more flexible	4.3634
MOUSE_BALO	Balovaptan	PHE189189	189	189	0.8049	80.4924	0.7640	20.4164	19.6524	loosened / more flexible	19.6524
MOUSE_BALO	Balovaptan	TRP206206	206	206	0.6347	63.4747	0.8448	20.7347	19.8899	loosened / more flexible	19.8899
MOUSE_BALO	Balovaptan	ALA207207	207	207	0.6861	68.6066	0.9385	20.8058	19.8674	loosened / more flexible	19.8674
MOUSE_BALO	Balovaptan	PHE209209	209	209	0.8356	83.5623	1.2167	24.0435	22.8267	loosened / more flexible	22.8267
MOUSE_BALO	Balovaptan	THR215215	215	215	0.7853	78.5344	0.9773	20.3644	19.3870	loosened / more flexible	19.3870
MOUSE_BALO	Balovaptan	TYR218218	218	218	0.9997	99.9720	0.8684	16.9517	16.0833	loosened / more flexible	16.0833
MOUSE_BALO	Balovaptan	VAL219219	219	219	0.9996	99.9580	0.7948	15.2973	14.5026	loosened / more flexible	14.5026
MOUSE_BALO	Balovaptan	MET222222	222	222	0.9997	99.9720	0.7153	11.4239	10.7086	loosened / more flexible	10.7086
MOUSE_BALO	Balovaptan	THR223223	223	223	0.9656	96.5581	0.7116	11.3334	10.6217	loosened / more flexible	10.6217
MOUSE_BALO	Balovaptan	VAL226226	226	226	0.1043	10.4278	0.6733	6.8012	6.1279	loosened / more flexible	6.1279
MOUSE_BALO	Balovaptan	PHE312312	312	312	0.9999	99.9920	0.7842	11.8599	11.0758	loosened / more flexible	11.0758
MOUSE_BALO	Balovaptan	PHE313313	313	313	0.9994	99.9440	0.9240	12.4045	11.4805	loosened / more flexible	11.4805
MOUSE_BALO	Balovaptan	GLN316316	316	316	0.9969	99.6940	1.2968	15.5356	14.2388	loosened / more flexible	14.2388
MOUSE_BALO	Balovaptan	VAL320320	320	320	0.1173	11.7278	2.2536	21.2801	19.0265	loosened / more flexible	19.0265
MOUSE_BALO	Balovaptan	TRP327327	327	327	0.2360	23.5975	5.7455	24.5543	18.8088	loosened / more flexible	18.8088
MOUSE_BALO	Balovaptan	GLU331331	331	331	0.1575	15.7457	3.5863	22.7653	19.1790	loosened / more flexible	19.1790
MOUSE_BALO	Balovaptan	THR335335	335	335	0.2738	27.3755	1.2341	16.2461	15.0120	loosened / more flexible	15.0120
MOUSE_BALO	Balovaptan	THR336336	336	336	0.6748	67.4827	1.3236	15.8582	14.5346	loosened / more flexible	14.5346
MOUSE_BALO	Balovaptan	ALA339339	339	339	0.9995	99.9540	0.9377	11.3139	10.3762	loosened / more flexible	10.3762
MOUSE_BALO	Balovaptan	LEU340340	340	340	0.9958	99.5780	1.0312	12.1618	11.1306	loosened / more flexible	11.1306
MOUSE_BALO	Balovaptan	SER343343	343	343	0.9539	95.3941	0.9129	8.3242	7.4113	loosened / more flexible	7.4113
MOUSE_UMF	UMF-504	VAL100100	100	100	0.1019	10.1858	0.6025	0.6315	0.0290	loosened / more flexible	0.0290
MOUSE_UMF	UMF-504	GLN104104	104	104	1.0000	100.0000	0.7102	0.8425	0.1323	loosened / more flexible	0.1323
MOUSE_UMF	UMF-504	VAL105105	105	105	0.8552	85.5183	0.6794	0.7815	0.1021	loosened / more flexible	0.1021
MOUSE_UMF	UMF-504	PRO107107	107	107	0.5202	52.0190	0.7548	1.3216	0.5667	loosened / more flexible	0.5667
MOUSE_UMF	UMF-504	GLN108108	108	108	0.9962	99.6200	0.8683	1.3360	0.4677	loosened / more flexible	0.4677
MOUSE_UMF	UMF-504	LYS128128	128	128	0.9988	99.8820	0.5821	0.6484	0.0663	loosened / more flexible	0.0663
MOUSE_UMF	UMF-504	GLN131131	131	131	1.0000	100.0000	0.6261	0.6615	0.0354	loosened / more flexible	0.0354
MOUSE_UMF	UMF-504	VAL132132	132	132	0.9787	97.8660	0.6157	0.6898	0.0741	loosened / more flexible	0.0741
MOUSE_UMF	UMF-504	MET135135	135	135	0.8436	84.3583	0.6196	0.7329	0.1134	loosened / more flexible	0.1134
MOUSE_UMF	UMF-504	PHE189189	189	189	0.9988	99.8820	0.7640	0.8524	0.0883	loosened / more flexible	0.0883
MOUSE_UMF	UMF-504	TRP206206	206	206	0.9447	94.4661	0.8448	1.0980	0.2532	loosened / more flexible	0.2532
MOUSE_UMF	UMF-504	ALA207207	207	207	0.9894	98.9400	0.9385	0.9248	-0.0136	stabilized / rigidified	0.0136
MOUSE_UMF	UMF-504	PHE209209	209	209	0.9924	99.2380	1.2167	1.5642	0.3474	loosened / more flexible	0.3474
MOUSE_UMF	UMF-504	THR215215	215	215	0.9876	98.7600	0.9773	1.1322	0.1549	loosened / more flexible	0.1549
MOUSE_UMF	UMF-504	TYR218218	218	218	0.9999	99.9880	0.8684	0.9496	0.0812	loosened / more flexible	0.0812
MOUSE_UMF	UMF-504	VAL219219	219	219	1.0000	100.0000	0.7948	0.8381	0.0433	loosened / more flexible	0.0433
MOUSE_UMF	UMF-504	MET222222	222	222	1.0000	99.9980	0.7153	0.9609	0.2456	loosened / more flexible	0.2456
MOUSE_UMF	UMF-504	THR223223	223	223	0.9999	99.9880	0.7116	1.0022	0.2905	loosened / more flexible	0.2905
MOUSE_UMF	UMF-504	VAL226226	226	226	0.1100	11.0018	0.6733	1.8399	1.1666	loosened / more flexible	1.1666
MOUSE_UMF	UMF-504	TRP309309	309	309	0.9992	99.9240	0.7982	0.7415	-0.0567	stabilized / rigidified	0.0567
MOUSE_UMF	UMF-504	PHE312312	312	312	0.9999	99.9940	0.7842	0.7861	0.0019	loosened / more flexible	0.0019
MOUSE_UMF	UMF-504	PHE313313	313	313	0.9968	99.6780	0.9240	0.8552	-0.0688	stabilized / rigidified	0.0688
MOUSE_UMF	UMF-504	GLN316316	316	316	1.0000	100.0000	1.2968	1.0496	-0.2472	stabilized / rigidified	0.2472
MOUSE_UMF	UMF-504	MET317317	317	317	0.1625	16.2477	1.4602	1.3226	-0.1376	stabilized / rigidified	0.1376
MOUSE_UMF	UMF-504	VAL320320	320	320	0.1236	12.3578	2.2536	2.1240	-0.1296	stabilized / rigidified	0.1296
MOUSE_UMF	UMF-504	THR335335	335	335	0.9583	95.8261	1.2341	1.3074	0.0734	loosened / more flexible	0.0734
MOUSE_UMF	UMF-504	THR338338	338	338	0.9370	93.7021	0.9885	1.0536	0.0650	loosened / more flexible	0.0650
MOUSE_UMF	UMF-504	ALA339339	339	339	0.9999	99.9880	0.9377	1.0808	0.1431	loosened / more flexible	0.1431
MOUSE_UMF	UMF-504	ALA342342	342	342	0.2663	26.6275	0.8927	1.0061	0.1134	loosened / more flexible	0.1134

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
MOUSE_BALO	Balovaptan	MOUSE_UMF	UMF-504	0.6111	22	7	7	0.9985	-0.2128	0.0033	-0.2434

Ligand stability flags

Run	Ligand	OverallCall	ProteinStateCall	BindingSiteCall	PossibleDissociation	FlagReasons	LigandRMSDMean_A	LigandRMSDFinal_A	InteractionLoadRatio_LastOverFirst
MOUSE_BALO	Balovaptan	binding-site flexibility increaser	similar compactness; lower global RMSD; globally more flexible	binding site loosened/more flexible	False		1.4673	1.4041
MOUSE_UMF	UMF-504	binding-site flexibility increaser	more compact; lower global RMSD	binding site loosened/more flexible	False		1.7108	1.7722

Run details

MOUSE_APO — state=APO — ligand=APO

Metrics

Metric	Value
family	MOUSE
state	APO
is_apo	True
ligand_display	APO
protein_rmsd_mean_A	3.7454
protein_rmsd_std_A	0.4606
protein_rmsd_final_A	3.5791
protein_rmsd_last_half_mean_A	3.9183
protein_rmsd_slope_A_per_ns	0.0019
protein_rmsf_mean_A	1.3588
protein_rmsf_std_A	1.3061
rg_mean_A	20.4762
rg_std_A	0.1301
rg_final_A	20.3275
rg_last_half_mean_A	20.5074
rg_slope_A_per_ns	0.0000
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/MOUSE_APO/Analysis_Results/Protein_RMSD.csv",
  "protein_rmsf_csvs": "/home/jxs794/MD_JOBS/Nahuel/MOUSE_APO/Analysis_Results/RMSF_V1AR_Mouse.csv;/home/jxs794/MD_JOBS/Nahuel/MOUSE_APO/Analysis_Results/RMSF_V1AR_Mouse_per_residue.csv",
  "radius_gyration_csv": "/home/jxs794/MD_JOBS/Nahuel/MOUSE_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
}

MOUSE_BALO — state=BALO — ligand=Balovaptan

Metrics

Metric	Value
family	MOUSE
state	BALO
is_apo	False
ligand_display	Balovaptan
protein_rmsd_mean_A	2.6260
protein_rmsd_std_A	0.3048
protein_rmsd_final_A	2.9260
protein_rmsd_last_half_mean_A	2.8388
protein_rmsd_slope_A_per_ns	0.0018
protein_rmsf_mean_A	18.3545
protein_rmsf_std_A	6.3912
rg_mean_A	20.3311
rg_std_A	0.1078
rg_final_A	20.3337
rg_last_half_mean_A	20.3193
rg_slope_A_per_ns	-0.0002
ligand_rmsd_mean_A	1.4673
ligand_rmsd_std_A	0.1314
ligand_rmsd_final_A	1.4041
ligand_rmsd_last_half_mean_A	1.4933
ligand_rmsd_slope_A_per_ns	0.0002
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	29
interaction_frame_count
interaction_load_first_half
interaction_load_last_half
interaction_load_ratio_last_over_first
used_framewise	False
framewise_file_size_mb	67.3507

Detected files

{
  "protein_rmsd_csv": "/home/jxs794/MD_JOBS/Nahuel/MOUSE_BALO/Analysis_Results/Protein_RMSD.csv",
  "protein_rmsf_csvs": "/home/jxs794/MD_JOBS/Nahuel/MOUSE_BALO/Analysis_Results/RMSF_V1AR_Mouse.csv;/home/jxs794/MD_JOBS/Nahuel/MOUSE_BALO/Analysis_Results/RMSF_V1AR_Mouse_per_residue.csv",
  "radius_gyration_csv": "/home/jxs794/MD_JOBS/Nahuel/MOUSE_BALO/Analysis_Results/Radius_of_Gyration_Protein_Ligand_Complex.csv",
  "ligand_rmsd_csv": "/home/jxs794/MD_JOBS/Nahuel/MOUSE_BALO/Analysis_Results/Balovaptan_Ligand_RMSD.csv",
  "ligand_rmsf_csv": "/home/jxs794/MD_JOBS/Nahuel/MOUSE_BALO/Analysis_Results/Balovaptan_Ligand_RMSF.csv",
  "bound_complex_rmsd_csv": null,
  "residue_summary_csv": "/home/jxs794/MD_JOBS/Nahuel/MOUSE_BALO/Analysis_Results/UNL_contact_frequency_filtered.csv",
  "interaction_type_summary_csv": "/home/jxs794/MD_JOBS/Nahuel/MOUSE_BALO/Analysis_Results/InteractionTypes_Summary.csv",
  "framewise_interaction_csv_skipped_by_default": "/home/jxs794/MD_JOBS/Nahuel/MOUSE_BALO/Analysis_Results/FilteredContacts_Framewise.csv",
  "contact_hover_framewise_csv": "/home/jxs794/MD_JOBS/Nahuel/MOUSE_BALO/Analysis_Results/FilteredContacts_Framewise.csv",
  "interaction_type_framewise_csv": "/home/jxs794/MD_JOBS/Nahuel/MOUSE_BALO/Analysis_Results/InteractionTypes_Framewise.csv",
  "ligand_structure_file": "/home/jxs794/MD_JOBS/Nahuel/MOUSE_BALO/UNL.cgenff.mol2"
}

MOUSE_UMF — state=UMF — ligand=UMF-504

Metrics

Metric	Value
family	MOUSE
state	UMF
is_apo	False
ligand_display	UMF-504
protein_rmsd_mean_A	2.8388
protein_rmsd_std_A	0.2595
protein_rmsd_final_A	3.2097
protein_rmsd_last_half_mean_A	2.9946
protein_rmsd_slope_A_per_ns	0.0013
protein_rmsf_mean_A	1.3780
protein_rmsf_std_A	0.9728
rg_mean_A	20.3279
rg_std_A	0.1386
rg_final_A	20.3769
rg_last_half_mean_A	20.2844
rg_slope_A_per_ns	-0.0003
ligand_rmsd_mean_A	1.7108
ligand_rmsd_std_A	0.1260
ligand_rmsd_final_A	1.7722
ligand_rmsd_last_half_mean_A	1.7261
ligand_rmsd_slope_A_per_ns	0.0000
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	29
interaction_frame_count
interaction_load_first_half
interaction_load_last_half
interaction_load_ratio_last_over_first
used_framewise	False
framewise_file_size_mb	71.0017

Detected files

{
  "protein_rmsd_csv": "/home/jxs794/MD_JOBS/Nahuel/MOUSE_UMF/Analysis_Results/Protein_RMSD.csv",
  "protein_rmsf_csvs": "/home/jxs794/MD_JOBS/Nahuel/MOUSE_UMF/Analysis_Results/RMSF_V1AR_Mouse.csv;/home/jxs794/MD_JOBS/Nahuel/MOUSE_UMF/Analysis_Results/RMSF_V1AR_Mouse_per_residue.csv",
  "radius_gyration_csv": "/home/jxs794/MD_JOBS/Nahuel/MOUSE_UMF/Analysis_Results/Radius_of_Gyration_Protein_Ligand_Complex.csv",
  "ligand_rmsd_csv": "/home/jxs794/MD_JOBS/Nahuel/MOUSE_UMF/Analysis_Results/UMF-504_Ligand_RMSD.csv",
  "ligand_rmsf_csv": "/home/jxs794/MD_JOBS/Nahuel/MOUSE_UMF/Analysis_Results/UMF-504_Ligand_RMSF.csv",
  "bound_complex_rmsd_csv": null,
  "residue_summary_csv": "/home/jxs794/MD_JOBS/Nahuel/MOUSE_UMF/Analysis_Results/UNL_contact_frequency_filtered.csv",
  "interaction_type_summary_csv": "/home/jxs794/MD_JOBS/Nahuel/MOUSE_UMF/Analysis_Results/InteractionTypes_Summary.csv",
  "framewise_interaction_csv_skipped_by_default": "/home/jxs794/MD_JOBS/Nahuel/MOUSE_UMF/Analysis_Results/FilteredContacts_Framewise.csv",
  "contact_hover_framewise_csv": "/home/jxs794/MD_JOBS/Nahuel/MOUSE_UMF/Analysis_Results/FilteredContacts_Framewise.csv",
  "interaction_type_framewise_csv": "/home/jxs794/MD_JOBS/Nahuel/MOUSE_UMF/Analysis_Results/InteractionTypes_Framewise.csv",
  "ligand_structure_file": "/home/jxs794/MD_JOBS/Nahuel/MOUSE_UMF/UNL.cgenff.mol2"
}