To explore the colletive motions of proteins and nucleic acids using Normal Mode Analysis (NMA) in internal coordinates (torsional space) just submit the atomic coordinates in PDB format (3.x). Backbone atoms N, CA and C are mandatory for dihedral angles definition. Maximum execution time is set to 10 minutes but you can use the standalone iMOD tool for longer runs.

Input your PDB file

Options CG CA C5 HA Email (optional)

Here, NMA calculations can be further customized. Please, check iMODS tutorial for details. Submit the atomic coordinates in PDB format (3.x), including backbone atoms N, CA and C for dihedral angles definition. Maximum execution time is set to 10 minutes but you can use the standalone iMOD tool for longer runs.

Input your PDB file

Options CG CA C5 HA Email (optional) #Modes Fix: Rand / SS  Elastic Network Model Sigmoid Tirion edNMA Cutoff  Clusters NO YES  Deform. NO YES Job name (optional)      Expert options (optional)

Feasible transition pathways between two different conformations of proteins or nucleic acids can be easily explored in this tab. The atomic coordinates of both structures should be provided 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. Maximum execution time is set to 10 minutes but you can use the standalone iMOD tool for longer runs.

Initial PDB file  Target PDB file

Options CG CA C5 HA Email (optional) #Modes Fix: Rand / SS  ΔCα-RMSD Alignment method User defined Local superimposition Global superimposition Job name (optional)      Expert options (optional)

Please enter your job ID*:
or select an example ---------------------------------------- NMA: Adenylate kinase (open) NMA: Calcium ATPase NMA: HIV-1 Protease NMA: Onconase Zymogen NMA: Nucleosome (Histones+DNA) NMA: GroEL cis-monomer NMA: GroEL trans-monomer NMA: GroEL/ES NMA: Bacterial RNA polymerase (prot) NMA: Bacterial RNA polymerase (full) NMA: Cowpea Chlorotic Mottle Virus NMA: Satellite Tobacco Mosaic Virus NMA: Microfilament (50-mer) MORPH: Adenylate kinase (homologs) MORPH: GroEL (1-mer) (open->closed) MORPH: GroEL (1-mer) (closed->open) MORPH: GroEL (ring) (closed->open) MORPH: Bacterial tRNA (1gtsB->3knjW) MORPH: Bacterial Flagellum (11-mer)

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