PyMACS dashboard

HUMAN 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: HUMAN_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

HUMAN_APO

Baseline protein state

Mean protein RMSD

3.120

Å, across available runs

Mean Rg

19.984

Å, compactness signal

Mean ligand RMSD

1.420

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/HUMAN, 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

HUMAN_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

HUMAN_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
HUMAN_APO	HUMAN	APO	True	APO	2.9589	3.3326	3.1848	0.0030	1.6395	1.0481	19.6962	19.5868	19.5331	-0.0008					0	False		True	True	True	False	False	False	False	0.5344	0.1609		False
HUMAN_BALO	HUMAN	BALO	False	Balovaptan	2.6903	3.2232	3.6052	0.0038	1.5418	0.9657	20.1524	20.1356	20.0276	-0.0002	1.4571	1.4450	1.4050	-0.0001	38	False	66.5624	True	True	True	True	True	True	True	0.5955	0.1217	0.1494	False
HUMAN_UMF	HUMAN	UMF	False	UMF-504	3.7119	3.8091	3.7160	0.0011	1.2385	0.9017	20.1039	20.1016	20.1453	0.0001	1.3836	1.3839	1.3126	-0.0000	27	False	74.4112	True	True	True	True	True	True	True	0.3408	0.1045	0.0613	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
HUMAN_APO	APO	APO	Yes	Yes	Yes	No	No	No	No	No		No
HUMAN_BALO	BALO	Balovaptan	Yes	Yes	Yes	Yes	No	Yes	Yes	Yes	LIG.cgenff.mol2	No	66.6
HUMAN_UMF	UMF	UMF-504	Yes	Yes	Yes	Yes	No	Yes	Yes	Yes	UNL.cgenff.mol2	No	74.4

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
HUMAN_BALO	Balovaptan	HUMAN_APO	2.9589	2.6903	-0.2685	3.3326	3.2232	-0.1093	3.1848	3.6052	0.4203	1.6395	1.5418	-0.0977	19.6962	20.1524	0.4562	19.5868	20.1356	0.5488	19.5331	20.0276	0.4945	0.0030	0.0038	0.0008	-0.0008	-0.0002	0.0006	more expanded; similar global RMSD
HUMAN_UMF	UMF-504	HUMAN_APO	2.9589	3.7119	0.7530	3.3326	3.8091	0.4765	3.1848	3.7160	0.5312	1.6395	1.2385	-0.4010	19.6962	20.1039	0.4077	19.5868	20.1016	0.5147	19.5331	20.1453	0.6122	0.0030	0.0011	-0.0020	-0.0008	0.0001	0.0010	more expanded; higher global RMSD; globally less 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
HUMAN_BALO	Balovaptan	26	-0.0035	-0.0570	0.3184	13	13	binding site similar to apo
HUMAN_UMF	UMF-504	23	-0.5805	-0.5582	0.6068	22	1	binding site rigidified/stabilized

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
HUMAN_BALO	Balovaptan	GLU5454	54	54	0.1838	18.3796	2.6119	2.4374	-0.1746	stabilized / rigidified	0.1746
HUMAN_BALO	Balovaptan	LEU5858	58	58	0.4319	43.1911	1.0501	1.9037	0.8536	loosened / more flexible	0.8536
HUMAN_BALO	Balovaptan	GLN104104	104	104	0.9999	99.9920	1.3594	1.4294	0.0700	loosened / more flexible	0.0700
HUMAN_BALO	Balovaptan	VAL105105	105	105	0.2247	22.4656	1.2647	1.4736	0.2089	loosened / more flexible	0.2089
HUMAN_BALO	Balovaptan	PRO107107	107	107	0.2724	27.2355	1.7791	1.9306	0.1515	loosened / more flexible	0.1515
HUMAN_BALO	Balovaptan	GLN108108	108	108	0.9972	99.7220	1.7766	2.0014	0.2248	loosened / more flexible	0.2248
HUMAN_BALO	Balovaptan	TRP111111	111	111	0.5438	54.3809	1.9249	2.3989	0.4740	loosened / more flexible	0.4740
HUMAN_BALO	Balovaptan	LYS128128	128	128	0.9049	90.4862	1.2119	0.7960	-0.4159	stabilized / rigidified	0.4159
HUMAN_BALO	Balovaptan	GLN131131	131	131	0.9888	98.8800	0.8640	0.9782	0.1143	loosened / more flexible	0.1143
HUMAN_BALO	Balovaptan	VAL132132	132	132	0.8223	82.2264	0.8938	1.1661	0.2723	loosened / more flexible	0.2723
HUMAN_BALO	Balovaptan	MET135135	135	135	0.8492	84.9223	0.9445	0.8676	-0.0769	stabilized / rigidified	0.0769
HUMAN_BALO	Balovaptan	GLN185185	185	185	0.7073	70.7326	1.9227	1.7977	-0.1250	stabilized / rigidified	0.1250
HUMAN_BALO	Balovaptan	PHE189189	189	189	0.9692	96.9221	3.6137	1.1513	-2.4624	stabilized / rigidified	2.4624
HUMAN_BALO	Balovaptan	TRP204204	204	204	0.4409	44.0871	1.7203	1.3538	-0.3665	stabilized / rigidified	0.3665
HUMAN_BALO	Balovaptan	ALA205205	205	205	0.4121	41.2072	1.4760	1.4328	-0.0432	stabilized / rigidified	0.0432
HUMAN_BALO	Balovaptan	PHE207207	207	207	0.9415	94.1481	1.7143	1.5234	-0.1909	stabilized / rigidified	0.1909
HUMAN_BALO	Balovaptan	SER213213	213	213	0.1117	11.1698	1.2461	1.2743	0.0281	loosened / more flexible	0.0281
HUMAN_BALO	Balovaptan	TYR216216	216	216	0.9398	93.9781	1.1902	1.0717	-0.1185	stabilized / rigidified	0.1185
HUMAN_BALO	Balovaptan	VAL217217	217	217	0.9988	99.8800	0.9686	0.9683	-0.0003	stabilized / rigidified	0.0003
HUMAN_BALO	Balovaptan	MET220220	220	220	0.9784	97.8380	0.9323	0.8989	-0.0335	stabilized / rigidified	0.0335
HUMAN_BALO	Balovaptan	THR221221	221	221	0.9756	97.5600	0.9410	0.8734	-0.0676	stabilized / rigidified	0.0676
HUMAN_BALO	Balovaptan	ILE224224	224	224	0.9581	95.8141	1.0077	0.8977	-0.1100	stabilized / rigidified	0.1100
HUMAN_BALO	Balovaptan	TRP304304	304	304	0.3075	30.7534	0.6999	1.4155	0.7155	loosened / more flexible	0.7155
HUMAN_BALO	Balovaptan	PHE307307	307	307	0.9988	99.8800	0.7772	1.0287	0.2515	loosened / more flexible	0.2515
HUMAN_BALO	Balovaptan	PHE308308	308	308	0.9966	99.6600	1.0221	1.4632	0.4411	loosened / more flexible	0.4411
HUMAN_BALO	Balovaptan	GLN311311	311	311	0.9887	98.8720	1.4138	1.7022	0.2884	loosened / more flexible	0.2884
HUMAN_UMF	UMF-504	GLN104104	104	104	1.0000	100.0000	1.3594	0.7931	-0.5662	stabilized / rigidified	0.5662
HUMAN_UMF	UMF-504	VAL105105	105	105	0.4387	43.8651	1.2647	0.7437	-0.5210	stabilized / rigidified	0.5210
HUMAN_UMF	UMF-504	GLN108108	108	108	1.0000	99.9960	1.7766	0.9570	-0.8196	stabilized / rigidified	0.8196
HUMAN_UMF	UMF-504	LYS128128	128	128	0.9633	96.3261	1.2119	0.6181	-0.5939	stabilized / rigidified	0.5939
HUMAN_UMF	UMF-504	GLN131131	131	131	1.0000	100.0000	0.8640	0.6111	-0.2528	stabilized / rigidified	0.2528
HUMAN_UMF	UMF-504	VAL132132	132	132	1.0000	99.9960	0.8938	0.5996	-0.2942	stabilized / rigidified	0.2942
HUMAN_UMF	UMF-504	MET135135	135	135	0.9999	99.9880	0.9445	0.5834	-0.3612	stabilized / rigidified	0.3612
HUMAN_UMF	UMF-504	GLN185185	185	185	0.9973	99.7340	1.9227	0.7542	-1.1685	stabilized / rigidified	1.1685
HUMAN_UMF	UMF-504	VAL188188	188	188	0.6315	63.1487	3.0403	0.7887	-2.2515	stabilized / rigidified	2.2515
HUMAN_UMF	UMF-504	PHE189189	189	189	0.9966	99.6620	3.6137	0.6594	-2.9543	stabilized / rigidified	2.9543
HUMAN_UMF	UMF-504	TRP204204	204	204	0.3487	34.8673	1.7203	0.9543	-0.7660	stabilized / rigidified	0.7660
HUMAN_UMF	UMF-504	ALA205205	205	205	0.9549	95.4881	1.4760	0.8381	-0.6379	stabilized / rigidified	0.6379
HUMAN_UMF	UMF-504	PHE207207	207	207	0.9815	98.1500	1.7143	1.5044	-0.2099	stabilized / rigidified	0.2099
HUMAN_UMF	UMF-504	SER213213	213	213	0.8322	83.2223	1.2461	1.5482	0.3021	loosened / more flexible	0.3021
HUMAN_UMF	UMF-504	TYR216216	216	216	0.9998	99.9760	1.1902	0.8123	-0.3779	stabilized / rigidified	0.3779
HUMAN_UMF	UMF-504	VAL217217	217	217	1.0000	100.0000	0.9686	0.7634	-0.2053	stabilized / rigidified	0.2053
HUMAN_UMF	UMF-504	MET220220	220	220	1.0000	99.9980	0.9323	0.7492	-0.1831	stabilized / rigidified	0.1831
HUMAN_UMF	UMF-504	THR221221	221	221	0.9999	99.9920	0.9410	0.8396	-0.1014	stabilized / rigidified	0.1014
HUMAN_UMF	UMF-504	ILE224224	224	224	0.9972	99.7200	1.0077	0.7729	-0.2348	stabilized / rigidified	0.2348
HUMAN_UMF	UMF-504	TRP304304	304	304	0.8029	80.2904	0.6999	0.5834	-0.1165	stabilized / rigidified	0.1165
HUMAN_UMF	UMF-504	PHE307307	307	307	0.9996	99.9560	0.7772	0.6081	-0.1692	stabilized / rigidified	0.1692
HUMAN_UMF	UMF-504	PHE308308	308	308	0.9999	99.9860	1.0221	0.6665	-0.3557	stabilized / rigidified	0.3557
HUMAN_UMF	UMF-504	GLN311311	311	311	0.9994	99.9400	1.4138	0.9007	-0.5131	stabilized / rigidified	0.5131

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
HUMAN_BALO	Balovaptan	HUMAN_UMF	UMF-504	0.6667	26	12	1	0.9989	-1.0216	0.0485	0.0736

Ligand stability flags

Run	Ligand	OverallCall	ProteinStateCall	BindingSiteCall	PossibleDissociation	FlagReasons	LigandRMSDMean_A	LigandRMSDFinal_A	InteractionLoadRatio_LastOverFirst
HUMAN_BALO	Balovaptan	no obvious instability flag	more expanded; similar global RMSD	binding site similar to apo	False		1.4571	1.4050
HUMAN_UMF	UMF-504	stable binding-site stabilizer	more expanded; higher global RMSD; globally less flexible	binding site rigidified/stabilized	False		1.3836	1.3126

Run details

HUMAN_APO — state=APO — ligand=APO

Metrics

Metric	Value
family	HUMAN
state	APO
is_apo	True
ligand_display	APO
protein_rmsd_mean_A	2.9589
protein_rmsd_std_A	0.5344
protein_rmsd_final_A	3.1848
protein_rmsd_last_half_mean_A	3.3326
protein_rmsd_slope_A_per_ns	0.0030
protein_rmsf_mean_A	1.6395
protein_rmsf_std_A	1.0481
rg_mean_A	19.6962
rg_std_A	0.1609
rg_final_A	19.5331
rg_last_half_mean_A	19.5868
rg_slope_A_per_ns	-0.0008
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/HUMAN_APO/Analysis_Results/Protein_RMSD.csv",
  "protein_rmsf_csvs": "/home/jxs794/MD_JOBS/Nahuel/HUMAN_APO/Analysis_Results/RMSF_AVPR1A.csv;/home/jxs794/MD_JOBS/Nahuel/HUMAN_APO/Analysis_Results/RMSF_AVPR1A_per_residue.csv",
  "radius_gyration_csv": "/home/jxs794/MD_JOBS/Nahuel/HUMAN_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
}

HUMAN_BALO — state=BALO — ligand=Balovaptan

Metrics

Metric	Value
family	HUMAN
state	BALO
is_apo	False
ligand_display	Balovaptan
protein_rmsd_mean_A	2.6903
protein_rmsd_std_A	0.5955
protein_rmsd_final_A	3.6052
protein_rmsd_last_half_mean_A	3.2232
protein_rmsd_slope_A_per_ns	0.0038
protein_rmsf_mean_A	1.5418
protein_rmsf_std_A	0.9657
rg_mean_A	20.1524
rg_std_A	0.1217
rg_final_A	20.0276
rg_last_half_mean_A	20.1356
rg_slope_A_per_ns	-0.0002
ligand_rmsd_mean_A	1.4571
ligand_rmsd_std_A	0.1494
ligand_rmsd_final_A	1.4050
ligand_rmsd_last_half_mean_A	1.4450
ligand_rmsd_slope_A_per_ns	-0.0001
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	38
interaction_frame_count
interaction_load_first_half
interaction_load_last_half
interaction_load_ratio_last_over_first
used_framewise	False
framewise_file_size_mb	66.5624

Detected files

{
  "protein_rmsd_csv": "/home/jxs794/MD_JOBS/Nahuel/HUMAN_BALO/Analysis_Results/Protein_RMSD.csv",
  "protein_rmsf_csvs": "/home/jxs794/MD_JOBS/Nahuel/HUMAN_BALO/Analysis_Results/RMSF_AVPR1A.csv;/home/jxs794/MD_JOBS/Nahuel/HUMAN_BALO/Analysis_Results/RMSF_AVPR1A_per_residue.csv",
  "radius_gyration_csv": "/home/jxs794/MD_JOBS/Nahuel/HUMAN_BALO/Analysis_Results/Radius_of_Gyration_Protein_Ligand_Complex.csv",
  "ligand_rmsd_csv": "/home/jxs794/MD_JOBS/Nahuel/HUMAN_BALO/Analysis_Results/Balovaptan_Ligand_RMSD.csv",
  "ligand_rmsf_csv": "/home/jxs794/MD_JOBS/Nahuel/HUMAN_BALO/Analysis_Results/Balovaptan_Ligand_RMSF.csv",
  "bound_complex_rmsd_csv": null,
  "residue_summary_csv": "/home/jxs794/MD_JOBS/Nahuel/HUMAN_BALO/Analysis_Results/LIG_contact_frequency_filtered.csv",
  "interaction_type_summary_csv": "/home/jxs794/MD_JOBS/Nahuel/HUMAN_BALO/Analysis_Results/InteractionTypes_Summary.csv",
  "framewise_interaction_csv_skipped_by_default": "/home/jxs794/MD_JOBS/Nahuel/HUMAN_BALO/Analysis_Results/FilteredContacts_Framewise.csv",
  "contact_hover_framewise_csv": "/home/jxs794/MD_JOBS/Nahuel/HUMAN_BALO/Analysis_Results/FilteredContacts_Framewise.csv",
  "interaction_type_framewise_csv": "/home/jxs794/MD_JOBS/Nahuel/HUMAN_BALO/Analysis_Results/InteractionTypes_Framewise.csv",
  "ligand_structure_file": "/home/jxs794/MD_JOBS/Nahuel/HUMAN_BALO/LIG.cgenff.mol2"
}

HUMAN_UMF — state=UMF — ligand=UMF-504

Metrics

Metric	Value
family	HUMAN
state	UMF
is_apo	False
ligand_display	UMF-504
protein_rmsd_mean_A	3.7119
protein_rmsd_std_A	0.3408
protein_rmsd_final_A	3.7160
protein_rmsd_last_half_mean_A	3.8091
protein_rmsd_slope_A_per_ns	0.0011
protein_rmsf_mean_A	1.2385
protein_rmsf_std_A	0.9017
rg_mean_A	20.1039
rg_std_A	0.1045
rg_final_A	20.1453
rg_last_half_mean_A	20.1016
rg_slope_A_per_ns	0.0001
ligand_rmsd_mean_A	1.3836
ligand_rmsd_std_A	0.0613
ligand_rmsd_final_A	1.3126
ligand_rmsd_last_half_mean_A	1.3839
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	27
interaction_frame_count
interaction_load_first_half
interaction_load_last_half
interaction_load_ratio_last_over_first
used_framewise	False
framewise_file_size_mb	74.4112

Detected files

{
  "protein_rmsd_csv": "/home/jxs794/MD_JOBS/Nahuel/HUMAN_UMF/Analysis_Results/Protein_RMSD.csv",
  "protein_rmsf_csvs": "/home/jxs794/MD_JOBS/Nahuel/HUMAN_UMF/Analysis_Results/RMSF_AVPR1A.csv;/home/jxs794/MD_JOBS/Nahuel/HUMAN_UMF/Analysis_Results/RMSF_AVPR1A_per_residue.csv",
  "radius_gyration_csv": "/home/jxs794/MD_JOBS/Nahuel/HUMAN_UMF/Analysis_Results/Radius_of_Gyration_Protein_Ligand_Complex.csv",
  "ligand_rmsd_csv": "/home/jxs794/MD_JOBS/Nahuel/HUMAN_UMF/Analysis_Results/UMF-504_Ligand_RMSD.csv",
  "ligand_rmsf_csv": "/home/jxs794/MD_JOBS/Nahuel/HUMAN_UMF/Analysis_Results/UMF-504_Ligand_RMSF.csv",
  "bound_complex_rmsd_csv": null,
  "residue_summary_csv": "/home/jxs794/MD_JOBS/Nahuel/HUMAN_UMF/Analysis_Results/UNL_contact_frequency_filtered.csv",
  "interaction_type_summary_csv": "/home/jxs794/MD_JOBS/Nahuel/HUMAN_UMF/Analysis_Results/InteractionTypes_Summary.csv",
  "framewise_interaction_csv_skipped_by_default": "/home/jxs794/MD_JOBS/Nahuel/HUMAN_UMF/Analysis_Results/FilteredContacts_Framewise.csv",
  "contact_hover_framewise_csv": "/home/jxs794/MD_JOBS/Nahuel/HUMAN_UMF/Analysis_Results/FilteredContacts_Framewise.csv",
  "interaction_type_framewise_csv": "/home/jxs794/MD_JOBS/Nahuel/HUMAN_UMF/Analysis_Results/InteractionTypes_Framewise.csv",
  "ligand_structure_file": "/home/jxs794/MD_JOBS/Nahuel/HUMAN_UMF/UNL.cgenff.mol2"
}