Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution models

Feig, Michael; Rotkiewicz, Piotr; Koliński, Andrzej; Skolnick, Jeffrey; Brooks, Charles L.

doi:10.1002/1097-0134(20001001)41:1<86::aid-prot110>3.0.co;2-y

Cited by 90 publications

(78 citation statements)

References 42 publications

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“…The results would certainly be somewhat better (i.e., lower cRMSD values) if the trajectory was clustered and a more elaborate fold selection performed [27]. Alternatively, the all-atom models could be reconstructed [28] and used for the selection of the best structure. Here, we opt for the most straightforward comparison of various methods.…”

Section: Resultsmentioning

confidence: 99%

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Protein fragment reconstruction using various modeling techniques

Boniecki

Rotkiewicz

Skolnick

et al. 2003

J Comput Aided Mol Des

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SummaryRecently developed reduced models of proteins with knowledge-based force fields have been applied to a specific case of comparative modeling. From twenty high resolution protein structures of various structural classes, significant fragments of their chains have been removed and treated as unknown. The remaining portions of the structures were treated as fixed -i.e., as templates with an exact alignment. Then, the missed fragments were reconstructed using several modeling tools. These included three reduced types of protein models: the lattice SICHO (Side Chain Only) model, the lattice CABS (Cα + Cβ + Side group) model and an off-lattice model similar to the CABS model and called REFINER. The obtained reduced models were compared with more standard comparative modeling tools such as MODELLER and the SWISS-MODEL server. The reduced model results are qualitatively better for the higher resolution lattice models, clearly suggesting that these are now mature, competitive and complementary (in the range of sparse alignments) to the classical tools of comparative modeling. Comparison between the various reduced models strongly suggests that the essential ingredient for the sucessful and accurate modeling of protein structures is not the representation of conformational space (lattice, off-lattice, all-atom) but, rather, the specificity of the force fields used and, perhaps, the sampling techniques employed. These conclusions are encouraging for the future application of the fast reduced models in comparative modeling on a genomic scale.

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Section: Resultsmentioning

confidence: 99%

“…Another possibility is to use fullatom models for the final evaluation [18,27]. Tools exist for rapid and accurate reconstruction of atomic details from the reduced model coordinates [28]. Of course, there is a 'brute force' solution to the problem of these poor quality models by allowing relaxation of the entire chain.…”

Section: Resultsmentioning

confidence: 99%

Protein fragment reconstruction using various modeling techniques

Boniecki

Rotkiewicz

Skolnick

et al. 2003

J Comput Aided Mol Des

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“…[44][45][46][47][48][49][50][51][52] In fact, comparative methods generally do not even attempt to model solvation effects. There are only a…”

Section: Combining Physics and Evolution To Improve Protein Structurementioning

confidence: 99%

Evolution and Physics in Comparative Protein Structure Modeling

et al. 2002

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From a physical perspective, the native structure of a protein is a consequence of physical forces acting on the protein and solvent atoms during the folding process. From a biological perspective, the native structure of proteins is a result of evolution over millions of years. Correspondingly, there are two types of protein structure prediction methods, de novo prediction and comparative modeling. We review comparative protein structure modeling and discuss the incorporation of physical considerations into the modeling process. A good starting point for achieving this aim is provided by comparative modeling by satisfaction of spatial restraints. Incorporation of physical considerations is illustrated by an inclusion of solvation effects into the modeling of loops.

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“…A total of 32 replicas were used and exponentially spaced from a reduced temperature T of 0.8 to 2.0, where T is normalized by a reference temperature such that b 21 5 k B T represents the energy unit (where k B is the Boltzmann constant). We set T 5 1 to represent the distribution of conformations modeled by the SICHO forcefield at 298 K. All-atom structures were reconstructed from the lattice simulations by using the MMTSB procedure developed by Feig et al 22 The lattice-based structures were refined by a combined application of steepest descent minimization and adopted-basis Newton-Raphson minimization for a total of 100 steps. To change the representation from lattice to all-atom model, we selected the CHARMM19 forcefield as a stepwise increase in resolution and modeled solvent effects during minimization by setting e 5 r. Nonbonded interaction cutoff parameters were set at values stated above.…”

Section: Methodsmentioning

confidence: 99%

Coarse‐grained lattice model simulations of sequence‐structure fitness of a ribosome‐inactivating protein

2007

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Many realistic protein‐engineering design problems extend beyond the computational limits of what is considered practical when applying all‐atom molecular‐dynamics simulation methods. Lattice models provide computationally robust alternatives, yet most are regarded as too simplistic to accurately capture the details of complex designs. We revisit a coarse‐grained lattice simulation model and demonstrate that a multiresolution modeling approach of reconstructing all‐atom structures from lattice chains is of sufficient accuracy to resolve the comparability of sequence‐structure modifications of the ricin A‐chain (RTA) protein fold. For a modeled structure, the unfolding–folding transition temperature was calculated from the heat capacity using either the potential energy from the lattice model or the all‐atom CHARMM19 force‐field plus a generalized Born solvent approximation. We found, that despite the low‐resolution modeling of conformational states, the potential energy functions were capable of detecting the relative change in the thermodynamic transition temperature that distinguishes between a protein design and the native RTA fold in excellent accord with reported experimental studies of thermal denaturation. A discussion is provided of different sequences fitted to the RTA fold and a possible unfolding model. © 2007 Wiley Periodicals, Inc. Biopolymers 89: 153–159, 2008.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

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Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution models

Cited by 90 publications

References 42 publications

Protein fragment reconstruction using various modeling techniques

Protein fragment reconstruction using various modeling techniques

Evolution and Physics in Comparative Protein Structure Modeling

Coarse‐grained lattice model simulations of sequence‐structure fitness of a ribosome‐inactivating protein

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