Algorithm for rapid reconstruction of protein backbone from alpha carbon coordinates

Milik, Mariusz; Koliński, Andrzej; Skolnick, Jeffrey

doi:10.1002/(sici)1096-987x(19970115)18:1<80::aid-jcc8>3.0.co;2-w

Cited by 37 publications

(47 citation statements)

References 14 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The backbone reconstruction method is based on a refined version o an algorithm proposed by Milik et al 5. The procedure requires four consecutive alpha carbon positions in order to rebuild the peptide bond atoms between the two central alpha carbons.…”

Section: Methodsmentioning

confidence: 99%

Fast procedure for reconstruction of full‐atom protein models from reduced representations

2008

Self Cite

View full text Add to dashboard Cite

We introduce PULCHRA, a fast and robust method for the reconstruction of full-atom protein models starting from a reduced protein representation. The algorithm is particularly suitable as an intermediate step between coarse grained model-based structure prediction and applications requiring an all-atom structure, such as molecular dynamics, protein-ligand docking, structure-based function prediction, or assessment of quality of the predicted structure. The accuracy of the method was tested on a set of high-resolution crystallographic structures, as well as on a set low-resolution protein decoys generated by a protein structure prediction algorithm TASSER. The method is implemented as a standalone program that is available for download from http://cssb.biology.gatech.edu/skolnick/files/PULCHRA

show abstract

Section: Methodsmentioning

confidence: 99%

Fast procedure for reconstruction of full‐atom protein models from reduced representations

2008

Self Cite

View full text Add to dashboard Cite

show abstract

“…The C β positions that are needed to evaluate these three terms are computed from the backbone of a conformation as in Milik et al 29 These three terms are crucial components of the coarse-grained energy function to guide the MC-SA exploration in the coarse-grained space. Description of the rest of the terms of the energy function together with further details on the length of an MC simulation and the update of the MC temperature in response to the number of accepted conformations during the simulation can be found in Supplemental Material.…”

Section: Methodsmentioning

confidence: 99%

Multiscale characterization of protein conformational ensembles

2009

View full text Add to dashboard Cite

We propose a multiscale exploration method to characterize the conformational space populated by a protein at equilibrium. The method efficiently obtains a large set of equilibrium conformations in two stages: first exploring the entire space at a coarse-grained level of detail, then narrowing a refined exploration to selected low-energy regions. The coarse-grained exploration periodically adds all-atom detail to selected conformations to ensure that the search leads to regions which maintain low energies in all-atom detail. The second stage reconstructs selected low-energy coarse-grained conformations in all-atom detail. A low-dimensional energy landscape associated with all-atom conformations allows focusing the exploration to energy minima and their conformational ensembles. The lowest energy ensembles are enriched with additional all-atom conformations through further multiscale exploration. The lowest energy ensembles obtained from the application of the method to three different proteins correctly capture the known functional states of the considered systems.

show abstract

“…Tested on 500 random decoy structures from the prediction benchmark. Uses a simple force field and steepest-descent minimization for backbone reconstruction based on a modified algorithm described by Milik et al 325 Available as a standalone command line application.…”

Section: Reconstruction Of Atomic Representation From Coarse-grained mentioning

confidence: 99%

Coarse-Grained Protein Models and Their Applications

et al. 2016

Self Cite

View full text Add to dashboard Cite

The traditional computational modeling of protein structure, dynamics, and interactions remains difficult for many protein systems. It is mostly due to the size of protein conformational spaces and required simulation time scales that are still too large to be studied in atomistic detail. Lowering the level of protein representation from all-atom to coarse-grained opens up new possibilities for studying protein systems. In this review we provide an overview of coarse-grained models focusing on their design, including choices of representation, models of energy functions, sampling of conformational space, and applications in the modeling of protein structure, dynamics, and interactions. A more detailed description is given for applications of coarse-grained models suitable for efficient combinations with all-atom simulations in multiscale modeling strategies.

show abstract

Algorithm for rapid reconstruction of protein backbone from alpha carbon coordinates

Cited by 37 publications

References 14 publications

Fast procedure for reconstruction of full‐atom protein models from reduced representations

Fast procedure for reconstruction of full‐atom protein models from reduced representations

Multiscale characterization of protein conformational ensembles

Coarse-Grained Protein Models and Their Applications

Contact Info

Product

Resources

About