A new peptide docking strategy using a mean field technique with mutually orthogonal Latin square sampling

Prasad, P. Arun; Gautham, N.

doi:10.1007/s10822-008-9216-5

Cited by 29 publications

(30 citation statements)

References 30 publications

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“…The PDZ-DocScheme [14] only used the peptide and protein side chains within 6 Å of the bound complex as flexible areas, whereas the rest of the protein was treated as a rigid body. A rapid sampling method based on mutually orthogonal Latin squares (MOLS) was developed to sample docking poses simultaneously during protein-peptide docking [15]. This method was also focused on the flexible peptide and ignored the flexibility of the receptor.…”

Section: Introductionmentioning

confidence: 99%

PaFlexPepDock: Parallel Ab-Initio Docking of Peptides onto Their Receptors with Full Flexibility Based on Rosetta

Chen

et al. 2014

PLoS ONE

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Structural information related to protein–peptide complexes can be very useful for novel drug discovery and design. The computational docking of protein and peptide can supplement the structural information available on protein–peptide interactions explored by experimental ways. Protein–peptide docking of this paper can be described as three processes that occur in parallel: ab-initio peptide folding, peptide docking with its receptor, and refinement of some flexible areas of the receptor as the peptide is approaching. Several existing methods have been used to sample the degrees of freedom in the three processes, which are usually triggered in an organized sequential scheme. In this paper, we proposed a parallel approach that combines all the three processes during the docking of a folding peptide with a flexible receptor. This approach mimics the actual protein–peptide docking process in parallel way, and is expected to deliver better performance than sequential approaches. We used 22 unbound protein–peptide docking examples to evaluate our method. Our analysis of the results showed that the explicit refinement of the flexible areas of the receptor facilitated more accurate modeling of the interfaces of the complexes, while combining all of the moves in parallel helped the constructing of energy funnels for predictions.

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Section: Introductionmentioning

confidence: 99%

PaFlexPepDock: Parallel Ab-Initio Docking of Peptides onto Their Receptors with Full Flexibility Based on Rosetta

Chen

et al. 2014

PLoS ONE

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“…A heuristic search of the potential energy surface of peptides in the binding grooves of (rigid) proteins was tested on a dataset of 56 complexes. 78 While all 20 tripeptides were successfully redocked, only 3 of the 36 larger (tetra, penta, hexa, and hepta) peptides could be redocked within 2 Å , suggesting that the sampling strategy needs further adaptation for the longer peptides.…”

Section: Structure-based Approaches For Peptide Design and Optimizationmentioning

confidence: 99%

Peptidic modulators of protein‐protein interactions: Progress and challenges in computational design

Rubinstein

Niv

2009

Biopolymers

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With the decline in productivity of drug‐development efforts, novel approaches to rational drug design are being introduced and developed. Naturally occurring and synthetic peptides are emerging as novel promising compounds that can specifically and efficiently modulate signaling pathways in vitro and in vivo. We describe sequence‐based approaches that use peptides to mimic proteins in order to inhibit the interaction of the mimicked protein with its partners. We then discuss a structure‐based approach, in which protein‐peptide complex structures are used to rationally design and optimize peptidic inhibitors. We survey flexible peptide docking techniques and discuss current challenges and future directions in the rational design of peptidic inhibitors. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 505–513, 2009.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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“…However, refinement is effective only if the approximate peptide backbone conformation within the receptor-binding site is given. Other methods dedicated to peptide docking have recently been developed but seem to be rather local as well [30], [31], [32], or restricted to very short peptides [33], [34].…”

Section: Introductionmentioning

confidence: 99%

Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Peptides onto Their Receptors

Raveh

London²,

Zimmerman³

et al. 2011

PLoS ONE

280

305

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Flexible peptides that fold upon binding to another protein molecule mediate a large number of regulatory interactions in the living cell and may provide highly specific recognition modules. We present Rosetta FlexPepDock ab-initio, a protocol for simultaneous docking and de-novo folding of peptides, starting from an approximate specification of the peptide binding site. Using the Rosetta fragments library and a coarse-grained structural representation of the peptide and the receptor, FlexPepDock ab-initio samples efficiently and simultaneously the space of possible peptide backbone conformations and rigid-body orientations over the receptor surface of a given binding site. The subsequent all-atom refinement of the coarse-grained models includes full side-chain modeling of both the receptor and the peptide, resulting in high-resolution models in which key side-chain interactions are recapitulated. The protocol was applied to a benchmark in which peptides were modeled over receptors in either their bound backbone conformations or in their free, unbound form. Near-native peptide conformations were identified in 18/26 of the bound cases and 7/14 of the unbound cases. The protocol performs well on peptides from various classes of secondary structures, including coiled peptides with unusual turns and kinks. The results presented here significantly extend the scope of state-of-the-art methods for high-resolution peptide modeling, which can now be applied to a wide variety of peptide-protein interactions where no prior information about the peptide backbone conformation is available, enabling detailed structure-based studies and manipulation of those interactions.

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A new peptide docking strategy using a mean field technique with mutually orthogonal Latin square sampling

Cited by 29 publications

References 30 publications

PaFlexPepDock: Parallel Ab-Initio Docking of Peptides onto Their Receptors with Full Flexibility Based on Rosetta

PaFlexPepDock: Parallel Ab-Initio Docking of Peptides onto Their Receptors with Full Flexibility Based on Rosetta

Peptidic modulators of protein‐protein interactions: Progress and challenges in computational design

Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Peptides onto Their Receptors

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