Protein structure prediction using basin-hopping

Prentiss, Michael C.; Wales, David J.; Wolynes, Peter G.

doi:10.1063/1.2929833

Cited by 42 publications

(48 citation statements)

References 44 publications

(56 reference statements)

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“…The Basin-Hopping method has been used to solve complex molecular systems (e.g., Prentiss et al 2008;Kim et al 2014) and is based on scanning several local minima to estimate the global minimum. When the solution was found, we ran a Levenberg-Marquardt algorithm of the MINPACK library (More 1978) for each parameter individually to adjust them to a better precision.…”

Section: Hapke Model On Disk-averaged Photometrymentioning

confidence: 99%

Spectrophotometric properties of the nucleus of comet 67P/Churyumov-Gerasimenko from the OSIRIS instrument onboard the ROSETTA spacecraft

Fornasier

Hasselmann

Barucci

et al. 2015

A&A

216

147

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Context. The Rosetta mission of the European Space Agency has been orbiting the comet 67P/Churyumov-Gerasimenko (67P) since August 2014 and is now in its escort phase. A large complement of scientific experiments designed to complete the most detailed study of a comet ever attempted are onboard Rosetta. Aims. We present results for the photometric and spectrophotometric properties of the nucleus of 67P derived from the OSIRIS imaging system, which consists of a Wide Angle Camera (WAC) and a Narrow Angle Camera (NAC). The observations presented here were performed during July and the beginning of August 2014, during the approach phase, when OSIRIS was mapping the surface of the comet with several filters at different phase angles (1.3• -54• ). The resolution reached up to 2.1 m/px. Methods. The OSIRIS images were processed with the OSIRIS standard pipeline, then converted into I/F radiance factors and corrected for the illumination conditions at each pixel using the Lommel-Seeliger disk law. Color cubes of the surface were produced by stacking registered and illumination-corrected images. Furthermore, photometric analysis was performed both on disk-averaged photometry in several filters and on disk-resolved images acquired with the NAC orange filter, centered at 649 nm, using Hapke modeling. Results. The disk-averaged phase function of the nucleus of 67P shows a strong opposition surge with a G parameter value of −0.13 ± 0.01 in the HG system formalism and an absolute magnitude H v (1, 1, 0) = 15.74 ± 0.02 mag. The integrated spectrophotometry in 20 filters covering the 250−1000 nm wavelength range shows a red spectral behavior, without clear absorption bands except for a potential absorption centered at ∼290 nm that is possibly due to SO 2 ice. The nucleus shows strong phase reddening, with disk-averaged spectral slopes increasing from 11%/(100 nm) to 16%/(100 nm) in the 1.3• −54• phase angle range. The geometric albedo of the comet is 6.5 ± 0.2% at 649 nm, with local variations of up to ∼16% in the Hapi region. From the disk-resolved images we computed the spectral slope together with local spectrophotometry and identified three distinct groups of regions (blue, moderately red, and red). The Hapi region is the brightest, the bluest in term of spectral slope, and the most active surface on the comet. Local spectrophotometry shows an enhancement of the flux in the 700−750 nm that is associated with coma emissions.

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Section: Hapke Model On Disk-averaged Photometrymentioning

confidence: 99%

Spectrophotometric properties of the nucleus of comet 67P/Churyumov-Gerasimenko from the OSIRIS instrument onboard the ROSETTA spacecraft

Fornasier

Hasselmann

Barucci

et al. 2015

A&A

216

147

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“…The resulting BH algorithm succeeds in locating both lower-energy mimina and conformations closer to the experimentally-determined native structure than MD with Simulated Annealing on small proteins. On sequences longer than 75 amino acids, the efficiency decreases [17].…”

Section: Introductionmentioning

confidence: 95%

“…In [17], the perturbation changes cartesian coordinates by values sampled uniformly at random over a small range. The minimization is implemented through a gradient descent of a selected coarse-grained energy function.…”

Section: Introductionmentioning

confidence: 99%

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Efficient basin hopping in the protein energy surface

Olson

Shehu

2012

2012 IEEE International Conference on Bioinformatics and Biomedicine

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The vast and rugged protein energy surface can be effectively represented in terms of local minima. The basin-hopping framework, where a structural perturbation is followed by an energy minimization, is particularly suited to obtaining this coarse-grained representation. Basin hopping is effective for small systems both in locating lower-energy minima and obtaining conformations near the native structure. The efficiency decreases for large systems. Our recent work improves efficiency on large systems through molecular fragment replacement. In this paper, we conduct a detailed investigation of two components in basin hopping, perturbation and minimization, and how they work in concert to affect the sampling of near-native local minima. We show that controlling the magnitude of perturbation jumps is related to the ability to effectively steer the exploration towards conformations near the protein native state. In minimization, we show that a simple greedy search is just as effective as Metropolis Monte Carlobased minimization. Finally, we show that an evolutionaryinspired approach based on the Pareto front is particularly effective in reducing the ensemble of sampled local minima and obtains a simpler representation of the probed energy surface.

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“…A common template among structure prediction protocols begins by sampling many local minima in the energy surface. Basin Hopping (BH) has emerged as a suitable framework for effectively sampling these coarsegrained local minima [2], [3]. BH consists of a series structural perturbations followed by minimizations, forming a trajectory of local minima with the Metropolis criterion biasing it towards increasingly low-energy minima.…”

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confidence: 99%

Jumping low, jumping high: Controlling hopping in the protein energy surface

Olson

Shehu

2012

2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops

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Corrcsponding AuthorKeywords-basin hopping; local minima; greedy local search; fragment-based assembly; protein native state.The protein conformational space is characterized as a multi-dimensional funnel-like energy surface with conformations corresponding to the native state around the energy basin [1]. The dimensionally and ruggedness of this energy surface are primary why computationally determining the biologically active or native state of a protein remains a difficult challenge. A common template among structure prediction protocols begins by sampling many local minima in the energy surface. Basin Hopping (BH) has emerged as a suitable framework for effectively sampling these coarsegrained local minima [2], [3]. BH consists of a series structural perturbations followed by minimizations, forming a trajectory of local minima with the Metropolis criterion biasing it towards increasingly low-energy minima.We conduct a detailed investigation of the perturbation and minimization components of our recently proposed BH framework [3]. We show that biasing the perturbation distance effectively controls the mean distance between consecutively sampled local minima. We then investigate the effect of controlling this minima distance on the ability of the BH framework to effectively capture near-native minima. In cases where unbiased perturbation leads to few small hops, biasing perturbation to create smaller hops in the energy surface leads to greater sampling of near-native minima. We compare a greedy local search to employing a MMC search with different effective temperatures for the minimization component. Employing a low non-zero temperature allows an MMC search to jump over small energy barriers and probe down to lower local minima. Analysis shows, however, that despite reaching lower energy levels, the longer MMC search is no more effective than simple greedy search at exploring near-native conformations.We investigate a novel multi-objective approach for filtering the resulting ensemble of sampled local minima to obtain a subset of interesting conformations for further refinement. Energy functions are computed as the weighted sum of multiple distinct energy terms and the selection of weights 978-1-4673-2747-3/12/$31.00 ©2012 IEEE 946 Figure 1: Energy vs. IRMSD to the native structure is shown for each conformation in the full ensemble and Pareto front.for these energy terms is a significant source of error for the energy function. We eliminate this source of error by taking the more nuanced approach of considering each energy term individually. As shown in Figure 1, the resulting Pareto front of non-dominated conformations represents at least a 94% reduction in ensemble size but still retains more "interesting" local minima suitable for further refinement as compared to a naive cutoff based only on total energy. ACKNOWLEDGMENTS

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Protein structure prediction using basin-hopping

Cited by 42 publications

References 44 publications

Spectrophotometric properties of the nucleus of comet 67P/Churyumov-Gerasimenko from the OSIRIS instrument onboard the ROSETTA spacecraft

Spectrophotometric properties of the nucleus of comet 67P/Churyumov-Gerasimenko from the OSIRIS instrument onboard the ROSETTA spacecraft

Efficient basin hopping in the protein energy surface

Jumping low, jumping high: Controlling hopping in the protein energy surface

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