Release Notes

v2.5.0 series come with new and improved sequence, structure, and dynamics analysis features. See release notes for details.

How to Cite

Bakan A, Meireles LM, Bahar I ProDy: Protein Dynamics Inferred from Theory and Experiments
Bioinformatics 2011 27(11):1575-1577.

Bakan A, Dutta A, Mao W, Liu Y, Chennubhotla C, Lezon TR, Bahar I Evol and ProDy for Bridging Protein Sequence Evolution and Structural Dynamics
Bioinformatics 2014 30(18):2681-2683.

Zhang S, Krieger JM, Zhang Y, Kaya C, Kaynak B, Mikulska-Ruminska K, Doruker P, Li H, Bahar I ProDy 2.0: Increased scale and scope after 10 years of protein dynamics modelling with Python
Bioinformatics 2021 37(20):3657-3659.

Python Module Index

a | c | d | e | k | m | p | s | t | u


	a
	`prody.apps`
	`prody.apps.evol_apps.evol_coevol`
	`prody.apps.evol_apps.evol_conserv`
	`prody.apps.evol_apps.evol_fetch`
	`prody.apps.evol_apps.evol_filter`
	`prody.apps.evol_apps.evol_merge`
	`prody.apps.evol_apps.evol_occupancy`
	`prody.apps.evol_apps.evol_rankorder`
	`prody.apps.evol_apps.evol_refine`
	`prody.apps.evol_apps.evol_search`
	`prody.apps.prody_apps.prody_align`
	`prody.apps.prody_apps.prody_anm`
	`prody.apps.prody_apps.prody_biomol`
	`prody.apps.prody_apps.prody_blast`
	`prody.apps.prody_apps.prody_catdcd`
	`prody.apps.prody_apps.prody_clustenm`
	`prody.apps.prody_apps.prody_contacts`
	`prody.apps.prody_apps.prody_fetch`
	`prody.apps.prody_apps.prody_gnm`
	`prody.apps.prody_apps.prody_pca`
	`prody.apps.prody_apps.prody_select`
	`prody.atomic`
	`prody.atomic.acceptor`
	`prody.atomic.angle`
	`prody.atomic.atom`
	`prody.atomic.atomgroup`
	`prody.atomic.atomic`
	`prody.atomic.atommap`
	`prody.atomic.bond`
	`prody.atomic.chain`
	`prody.atomic.crossterm`
	`prody.atomic.dihedral`
	`prody.atomic.donor`
	`prody.atomic.fields`
	`prody.atomic.flags`
	`prody.atomic.functions`
	`prody.atomic.hierview`
	`prody.atomic.improper`
	`prody.atomic.nbexclusion`
	`prody.atomic.pointer`
	`prody.atomic.residue`
	`prody.atomic.segment`
	`prody.atomic.select`
	`prody.atomic.selection`
	`prody.atomic.subset`

	c
	`prody.chromatin`
	`prody.chromatin.cluster`
	`prody.chromatin.functions`
	`prody.chromatin.hic`
	`prody.chromatin.norm`
	`prody.chromatin.straw`
	`prody.compounds`
	`prody.compounds.bird`
	`prody.compounds.ccd`
	`prody.compounds.functions`
	`prody.compounds.pdbligands`

	d
	`prody.database`
	`prody.database.cath`
	`prody.database.dali`
	`prody.database.goa`
	`prody.database.pfam`
	`prody.database.quartataweb`
	`prody.database.uniprot`
	`prody.domain_decomposition`
	`prody.domain_decomposition.spectrus`
	`prody.dynamics`
	`prody.dynamics.adaptive`
	`prody.dynamics.analysis`
	`prody.dynamics.anm`
	`prody.dynamics.compare`
	`prody.dynamics.editing`
	`prody.dynamics.essa`
	`prody.dynamics.exanm`
	`prody.dynamics.exgnm`
	`prody.dynamics.functions`
	`prody.dynamics.gamma`
	`prody.dynamics.gnm`
	`prody.dynamics.heatmapper`
	`prody.dynamics.imanm`
	`prody.dynamics.mechstiff`
	`prody.dynamics.mode`
	`prody.dynamics.modeset`
	`prody.dynamics.nma`
	`prody.dynamics.nmdfile`
	`prody.dynamics.pca`
	`prody.dynamics.perturb`
	`prody.dynamics.plotting`
	`prody.dynamics.rtb`
	`prody.dynamics.sampling`
	`prody.dynamics.signature`
	`prody.dynamics.vmdfile`

	e
	`prody.ensemble`
	`prody.ensemble.conformation`
	`prody.ensemble.ensemble`
	`prody.ensemble.functions`
	`prody.ensemble.pdbensemble`

	k
	`prody.kdtree`
	`prody.kdtree.kdtree`

	m
	`prody.measure`
	`prody.measure.contacts`
	`prody.measure.measure`
	`prody.measure.transform`

	p
	`prody`
	`prody.proteins`
	`prody.proteins.blastpdb`
	`prody.proteins.ciffile`
	`prody.proteins.compare`
	`prody.proteins.dssp`
	`prody.proteins.emdfile`
	`prody.proteins.functions`
	`prody.proteins.header`
	`prody.proteins.interactions`
	`prody.proteins.localpdb`
	`prody.proteins.pdbclusters`
	`prody.proteins.pdbfile`
	`prody.proteins.starfile`
	`prody.proteins.stride`
	`prody.proteins.wwpdb`

	s
	`prody.sequence`
	`prody.sequence.analysis`
	`prody.sequence.msa`
	`prody.sequence.msafile`
	`prody.sequence.plotting`
	`prody.sequence.sequence`

	t
	`prody.trajectory`
	`prody.trajectory.dcdfile`
	`prody.trajectory.frame`
	`prody.trajectory.psffile`
	`prody.trajectory.trajbase`
	`prody.trajectory.trajectory`
	`prody.trajectory.trajfile`

	u
	`prody.utilities`
	`prody.utilities.catchall`
	`prody.utilities.checkers`
	`prody.utilities.doctools`
	`prody.utilities.drawtools`
	`prody.utilities.eigtools`
	`prody.utilities.laptools`
	`prody.utilities.logger`
	`prody.utilities.misctools`
	`prody.utilities.pathtools`
	`prody.utilities.seqtools`
	`prody.utilities.settings`
	`prody.utilities.TreeConstruction`