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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


No version available

Documentation


Maintainer


  • person_outline Dahlia Weiss

Publication for Climber

Climber citations

 (5)
call_split

T7 RNA polymerase translocation is facilitated by a helix opening on the fingers domain that may also prevent backtracking

2017
Nucleic Acids Res
PMCID: 5737862
PMID: 28575393
DOI: 10.1093/nar/gkx495
call_split See protocol

[…] Based on the modeled pre- and post-trans states of the T7 RNAP elongation complexes (ECs), we first performed a Climber simulation () to obtain an initial low-energy translocation pathway. The conformations generated by the above-mentioned Climber simulation were then used as the initial seeds for the subsequen […]

call_split

Prediction and validation of protein intermediate states from structurally rich ensembles and coarse grained simulations

2016
Nat Commun
PMCID: 5013691
PMID: 27578633
DOI: 10.1038/ncomms12575
call_split See protocol

[…] nd-states ENM potential functions while iMODS interpolates in the dihedral angle space. We also compare with the non-linear atomistic algorithms NMSIM, which uses a complex three-steps procedure, and Climber, based on the molecular mechanics ENCAD potential. All the methods were run with their default parameters (See and ).For the non-linear eBDIMS and Climber, trajectories were computed in both […]

library_books

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics

2016
PLoS Comput Biol
PMCID: 4849799
PMID: 27124275
DOI: 10.1371/journal.pcbi.1004619

[…] ] is used to compute a series of steepest descent paths from saddle points to nearest minima to connect two structures of interest with a continuous curve in the conformation space. Similarly, in the Climber method [,], a restraining energy depends linearly on the distance deviation between the current conformation and the target conformation in a way that allows full flexibility and enables the p […]

library_books

Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue

2016
Nat Commun
PMCID: 4838855
PMID: 27091704
DOI: 10.1038/ncomms11244

[…] cing an rG:dG mismatched base pair in the active site and removing the backtracked nucleotides from the crystal structure (PDB ID: 3GTG). Next, we obtained the initial backtracking pathways using the Climber algorithm, which is designed to search for the low-energy pathways connecting two conformational states. To take into account the possibility of both stepwise and concerted mechanisms, we gene […]

library_books

MMB GUI: a fast morphing method demonstrates a possible ribosomal tRNA translocation trajectory

2015
Nucleic Acids Res
PMCID: 4705676
PMID: 26673695
DOI: 10.1093/nar/gkv1457

[…] ethod in the other cases. Concerning performances on Ca2+-ATPase and Rnase III, where MMB ranks first and second, Weiss and Levitt report better scores when using extreme parameters for their method, Climber. They obtained improvement scores of 16% and 48% respectively but with very long simulations. NOMAD-Ref ranked first on RNase III with 50% improvement but produced an erratic trajectory. In co […]

Citations

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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.

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