Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates

Gront, Dominik; Kmiecik, Sebastian; Koliński, Andrzej

doi:10.1002/jcc.20624

Cited by 111 publications

(108 citation statements)

References 20 publications

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“…Since a procedure exists for a fast and accurate protein chain rebuilding 44 with subsequent all-atom refinement and model assessment 45 , the proposed method should be applicable to detailed computational studies of long-time dynamics of biomolecular systems. An example of such multiscale modeling is schematically illustrated in Fig.…”

Section: Discussionmentioning

confidence: 99%

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Folding pathway of the B1 domain of protein G explored by a multiscale modeling

Kolinski¹

2007

SciVee

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SummaryThe understanding of the folding mechanisms of single domain proteins is an essential step in the understanding of protein folding in general. Recently, we developed a mesoscopic CABS protein model which was successfully applied in protein structure prediction, studies of protein thermodynamics and modeling of protein complexes. In the present research this model is employed in a detailed characterization of the folding process of a simple globular protein, the B1 domain of IgG-binding protein G (GB1). There is a vast body of experimental facts and theoretical findings for this protein. Performing unbiased, ab initio simulations, we demonstrated that the GB1 folding proceeds via the successive formation of an extended folding nucleus, followed by slow structure fine-tuning. Remarkably, a subset of native interactions drives the folding from the very beginning. The emerging comprehensive picture of GB1 folding perfectly matches and extends the previous experimental and theoretical studies.

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Section: Discussionmentioning

confidence: 99%

“…5) consisted of the following steps. First, the missing backbone atoms were reconstructed using the BBQ algorithm 44 . Subsequently, the side-chain rotamers were added using SCWRL 48 .…”

Section: Multiscale Modelingmentioning

confidence: 99%

Folding pathway of the B1 domain of protein G explored by a multiscale modeling

Kolinski¹

2007

SciVee

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“…To use an atom-level energy function, we also need to build the coordinates of other atoms. Given a C a trace, there are many methods that can build the coordinates for the main chain and C b atoms (Gront et al, 2007;Holm and Sander, 1991;Maupetit et al, 2000). To save computing time, we want a method that is both accurate and efficient.…”

Section: Building Backbone Atomsmentioning

confidence: 99%

“…To save computing time, we want a method that is both accurate and efficient. We choose to use a method similar to BBQ (Gront et al, 2007). The original BBQ method can only build coordinates for the backbone N, C, and O atoms.…”

Section: Building Backbone Atomsmentioning

confidence: 99%

A Probabilistic and Continuous Model of Protein Conformational Space for Template-Free Modeling

Zhao

Peng

DeBartolo

et al. 2010

Journal of Computational Biology

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One of the major challenges with protein template-free modeling is an efficient sampling algorithm that can explore a huge conformation space quickly. The popular fragment assembly method constructs a conformation by stringing together short fragments extracted from the Protein Data Base (PDB). The discrete nature of this method may limit generated conformations to a subspace in which the native fold does not belong. Another worry is that a protein with really new fold may contain some fragments not in the PDB. This article presents a probabilistic model of protein conformational space to overcome the above two limitations. This probabilistic model employs directional statistics to model the distribution of backbone angles and 2 nd -order Conditional Random Fields (CRFs) to describe sequenceangle relationship. Using this probabilistic model, we can sample protein conformations in a continuous space, as opposed to the widely used fragment assembly and lattice model methods that work in a discrete space. We show that when coupled with a simple energy function, this probabilistic method compares favorably with the fragment assembly method in the blind CASP8 evaluation, especially on alpha or small beta proteins. To our knowledge, this is the first probabilistic method that can search conformations in a continuous space and achieves favorable performance. Our method also generated three-dimensional (3D) models better than template-based methods for a couple of CASP8 hard targets. The method described in this article can also be applied to protein loop modeling, model refinement, and even RNA tertiary structure prediction.

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“…The BBQ (Backbone Building from Quadrilaterals) method (Gront et al, 2007) is an algorithm for protein backbone reconstruction that comprises high computational efficiency and accuracy. It considers a fragment with four contiguous amino acids as quadrilateral.…”

Section: Previous Workmentioning

confidence: 99%

Prediction of Protein Backbone Structure by Preference Classification with SVM

Yang

Chen

Huang

Proceedings of the 9th CONTECSI International Conference on Information Systems and Technology Management CONTECSI

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Given the primary sequence of a protein and its α-carbon coordinates, the allatom protein backbone reconstruction problem (PBRP) is to reconstruct the 3D coordinates of all atoms, including N, C, and O atoms on the backbone. A variety of methods for solving PBRP have been proposed, such as Adcock's method, SABBAC, BBQ, and Chang's methods. In this paper, we involve BBQ (Backbone Building from Quadrilaterals) and Chang's method as our candidate prediction tools. Then, we apply a tool preference classification with support vector machine (SVM) to determine which tool is more suitable for solving PBRP. According to the preference classification result, a proper prediction tool, either BBQ or Chang's method, is used to construct the atom of the target protein. Thus, after combining the results of all atoms, the backbone structure of the target protein is reconstructed. The three data sets of our experiments were extracted from CASP7, CASP8, and CASP9, which consists of 29, 24, and 55 proteins, respectively. The data sets contain only the proteins composed of standard amino acids. We improve the average RMSDs of BBQ results from 0.3955 to 0.3835 in CASP7, from 0.4437 to 0.4313 in CASP8, and from 0.4133 to 0.3691 in CASP9.

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Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates

Cited by 111 publications

References 20 publications

Folding pathway of the B1 domain of protein G explored by a multiscale modeling

Folding pathway of the B1 domain of protein G explored by a multiscale modeling

A Probabilistic and Continuous Model of Protein Conformational Space for Template-Free Modeling

Prediction of Protein Backbone Structure by Preference Classification with SVM

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