Climber statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Conformational transition modeling chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

Climber specifications

Information


Unique identifier OMICS_14353
Name Climber
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A protein structure.
Input format PDB
Operating system Unix/Linux
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

Versioning


Add your version

Documentation


Maintainer


  • person_outline Dahlia Weiss <>

Publication for Climber

Climber in publications

 (4)
PMCID: 5737862
PMID: 28575393
DOI: 10.1093/nar/gkx495

[…] changes involved in the translocation., based on the modeled pre- and post-trans structures, we first obtained an initial low-energy translocation pathway using a modified version of the climber algorithm (). we selected the fingers domain (residues from 554 to 812) and all dna/rna chains as the morphed regions since these regions undergo substantial conformational changes […]

PMCID: 5013691
PMID: 27578633
DOI: 10.1038/ncomms12575

[…] for ebdims pathway validation (see further examples in and ). the trajectories were compared with linear (nomad-ref, minactpath and ienm) and non-linear path-sampling algorithms (imods, nmsims and climber) (). we also created ensembles along the lowest frequency nms to study intrinsic motions. the apo-like, resting or inactive form was the reference for pca; all analyses focused on the two […]

PMCID: 4849799
PMID: 27124275
DOI: 10.1371/journal.pcbi.1004619

[…] are shown in ., morphing- and string-based methods provide an alternative way to compute transition trajectories. morphing-based methods include molmov [], fatcat [], nomad-ref [], minaction [], climber [], and more. in climber, the interresidue distances in a given start structure are pulled towards distances in the goal structure, using harmonic restraints incorporated in a pseudo-energy […]

PMCID: 4838855
PMID: 27091704
DOI: 10.1038/ncomms11244

[…] at 310k using gromacs 4.5 (ref. ; see for more details of the model construction)., we proposed two models of backtracking: a concerted and a stepwise model. for the concerted model, we applied the climber algorithm to generate the pathways along pre-translocation → backtracked states, as well as its reverse route: backtracked → pre-translocation states. for the stepwise model, the initial […]


To access a full list of publications, you will need to upgrade to our premium service.

Climber institution(s)
Department of Structural Biology, Stanford Medical School, Stanford, CA, USA
Climber funding source(s)
This work was supported by a Simbios student fellowship, by the National Institutes of Health (NIH) through the NIH Roadmap for Medical Research Grant U54 GM072970, by a Simbios NIH Award GM-63817 and by the National Science Foundation award CNS-0619926.

Climber reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Climber