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PULCHRA specifications


Unique identifier OMICS_25467
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Some atom coordinates.
Input format PDB
Output data Some full-atom files.
Output format PDB
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Stability Stable
Maintained No


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Publication for PULCHRA

PULCHRA citations


Dissecting Structure Encoded Determinants of Allosteric Cross Talk between Post Translational Modification Sites in the Hsp90 Chaperones

Sci Rep
PMCID: 5932063
PMID: 29720613
DOI: 10.1038/s41598-018-25329-4
call_split See protocol

[…] landscapes of the hsp90 proteins in a coarse-grained representation. the coarse-grained conformational ensembles of the hsp90 structures were then subjected to all-atom reconstruction using pulchra method and cg2aa tool that derived atomistic structures from simulation trajectories. the all-atom conformations were additionally optimized using the 3drefine method that utilizes […]


Conformational shift in the closed state of GroEL induced by ATP binding triggers a transition to the open state

Biophys Physicobiol
PMCID: 5042161
PMID: 27924266
DOI: 10.2142/biophysico.13.0_127

[…] only the lowest mode. remaining four low modes were included as perturbation terms about the lowest mode,, full atom structures except hydrogen atoms of the two conformations were reconstructed on pulchra [], and, heavy-atom rmsds between each of these reconstructed structures and the open state were calculated. out of the reconstructed two structures, the one with the smaller rmsd was chosen […]


Molecular dynamics simulation and bioinformatics study on chloroplast stromal ridge complex from rice (Oryza sativa L.)

BMC Bioinformatics
PMCID: 4709881
PMID: 26753869
DOI: 10.1186/s12859-016-0877-0

[…] cg protein representation, four steps were used according from the protocol described by sansom and coworkers []. firstly, the backbone of the protein was grown from the cg cα particles using the pulchra algorithm []. secondly, the missing side chain atoms of the protein were added using in modeller []. note that the advantage of these two steps is to preserve the original coordinates […]


Molecular Dynamics Simulations of the Bacterial UraA H+ Uracil Symporter in Lipid Bilayers Reveal a Closed State and a Selective Interaction with Cardiolipin

PLoS Comput Biol
PMCID: 4346270
PMID: 25729859
DOI: 10.1371/journal.pcbi.1004123

[…] at lipid fragments with the corresponding cg fragments from an energy-minimized library of atomistic lipid conformations. the protein backbone is reconstructed by the cg backbone trace using pulchra [] and the side chains using modeller [,]. atomistic molecular dynamics (at-md) simulations were performed using the gromos96 53a6 force field that has been widely used in simulation studies […]


A three dimensional visualisation approach to protein heavy atom structure reconstruction

BMC Struct Biol
PMCID: 4302604
PMID: 25551190
DOI: 10.1186/s12900-014-0027-8

[…] and/or all-atom model of the folded protein, based on the knowledge of the positions of the central cα atoms only. both knowledge-based approaches such and maxsprout [] and de novo methods including pulchra [] and remo [] have been developed, to try and resolve the cα- trace problem. in the case of the backbone atoms, the geometric algorithm introduced by purisima and scheraga [], […]


Molecular Dynamic Simulation of the Self Assembly of DAP12 NKG2C Activating Immunoreceptor Complex

PLoS One
PMCID: 4141757
PMID: 25148259
DOI: 10.1371/journal.pone.0105560

[…] (at) model was done in two steps as previous studies described , . briefly, the representative dap12-nkg2c trimer structure was clustered from cg-md trajectories and converted to an at model by pulchra software initially; secondly, this at model was inserted into a pre-equilibrated atomistic model of lipid bilayer using the inflategro method . the system was subjected to 1000 steps […]

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PULCHRA institution(s)
Burnham Institute for Medical Research, La Jolla, CA, USA; Center for the Study of Systems Biology, Georgia Institute of Technology, Atlanta, GA, USA
PULCHRA funding source(s)
Supported by NIH grant No. GM-37408 of the Division of General Medical Sciences of the National Institutes of Health.

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