iMODS
To explore the colletive motions of proteins and nucleic acids using NMA in internal coordinates (torsional space) just submit the PDB-ID or the atomic coordinates in PDB format (3.x). Backbone atoms N, CA and C are mandatory for dihedral angles definition.



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Here, NMA calculations can be further customized. Please, check iMODS tutorial for details. Submit either the PDB-ID or the atomic coordinates in PDB format (3.x), including backbone atoms N, CA and C for dihedral angles definition.



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Cutoff



    

Feasible transition pathways between two different conformations of proteins or nucleic acids can be easily explored in this tab. Both structures should be provided either as PDB-ID or atomic coordinates (in PDB format 3.x), including backbone atoms N, CA and C for dihedral angles definition. Homologue macromolecules can be processed, i.e. 100% sequence identity is not mandatory. Please, check iMODS tutorial for details.




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or select an example

Feel free to explore any of the precomputed examples! Please, email us if you want to share here any of your jobs.


NMA: Adenylate Kinase (open)

NMA: Calcium ATPase

NMA: Nucleosome Core (Histones/DNA)

MORPH: Bacterial Flagellum (R->L)

NMA: GroEL/ES

MORPH: Adenylate Kinase (homologs)

MORPH: Bacterial tRNA

NMA: GroEL cis-monomer

MORPH: GroEL ring (trans->cis)

MORPH: GroEL monomer (trans->cis)

NMA: GroEL trans-monomer

NMA: Onconase Zymogen

NMA: Cowpea Chlorotic Mottle Virus

NMA: Satellite Tobacco Mosaic Virus

NMA: HIV-1 Protease

MORPH: GroEL monomer (cis->trans)

NMA: Bacterial RNA polymerase (protein)

NMA: Bacterial RNA pol. (prot.+RNA+DNA)

iMODS

López-Blanco JR, Aliaga JI, Quintana-Ortí ES and Chacón P. (2014) iMODS: Internal coordinates normal mode analysis server. Nucleic acids research. 42:W271-6.

iMod

López-Blanco JR, Garzón JI, Chacón P. (2011) iMod: multipurpose normal mode analysis in internal coordinates. Bioinformatics. 27 (20): 2843-2850.

Deformability

Kovacs J., P. Chacón, R. Abagyan. (2004) Predictions of Protein Flexibility: First Order Measures. PROTEINS: Structure, Function, and Bioinformatics. Proteins. 56(4):661-8

Go to Chaconlab.org iMODS Tutorial