A multibody, whole‐residue potential for protein structures, with testing by Monte Carlo simulated annealing

Mayewski, Stefan

doi:10.1002/prot.20397

Cited by 17 publications

(20 citation statements)

References 83 publications

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“…One popular method to consider two residue sidechains in contact is to require the sidechain center/C a atom distance to be less than a predetermined threshold. [9][10][11]18,95 Another popular method is to require the existence of a pair of nonhydrogen atoms from residues i, j to be within a cutoff distance, 25,27,32,96 such as 5 Å . We previously developed the ADC method to evaluate the contact.…”

Section: Sidechain Contact Model: Atom Distance Criterion (Adc)mentioning

confidence: 99%

Understanding on the residue contact network using the log‐normal cluster model and the multilevel wheel diagram

Sun

2010

Biopolymers

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Residue clusters play essential role in stabilizing protein structures in the form of complex networks. We show that the cluster sizes in a native protein follow the log-normal distribution for a dataset consisting of 424 proteins. To our knowledge, this is the first time of such fitting for the native structures. Based on log-normal model, the asymptotically increasing mean cluster sizes produce a critical protein chain length of about 200 amino acids, beyond which length most globular proteins have nearly the same mean cluster sizes. This suggests that the larger proteins use a different packing mechanism than the smaller proteins. We confirmed the scale-free property of the residue contact network for most of the protein structures in the dataset, although the violations were observed for the tightly packed proteins. Residue cluster network wheel (RCNW) is proposed to visualize the relationship between the multiple properties of the residue network such as the cluster size, the residue types and contacts, and the flexibility of the residue. We noticed that the residues with large cluster size have smaller Calpha displacement measured using the normal mode analysis.

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Section: Sidechain Contact Model: Atom Distance Criterion (Adc)mentioning

confidence: 99%

Understanding on the residue contact network using the log‐normal cluster model and the multilevel wheel diagram

Sun

2010

Biopolymers

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“…In addition to residue distance dependence studies [14,15], recent work investigated the effect of relative orientations on contact energy [16,17]. In order to include the influence of multi-residue interactions and local environment dependence, tri-residue [18][19][20], four-residue [21][22][23][24][25][26][27][28][29] and the secondary structure related energy [30] have been studied recently.…”

Section: Introductionmentioning

confidence: 99%

“…Two residue sidechains are considered in contact if the sidechain center or the C atom distance is less than a predetermined threshold distance[1-3, 13,24]. A commonly used sidechain center distance threshold is 6.5 Å[2, 3,17].…”

Section: Introductionmentioning

confidence: 99%

Effect of sidechain anisotropy on residue contact determination

Sun

2009

2009 IEEE International Conference on Bioinformatics and Biomedicine Workshop

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The criteria used to determine the residue contact is a fundamental factor in deriving knowledge-based mean force potential energy for protein structures. A commonly used criterion for two residues in contact is to require the sidechain center distance or the C atom distance to be within a predetermined cutoff distance. However, the anisotropic nature of the sidechains can result in error in the counting of the contact pairs. This study compared three sidechain contact models: the surface-to-surface model based on atom distance criteria (ADC), the isotropic sphere sidechain (ISS) model and the anisotropic ellipsoid sidechain (AES) model. A test using 424 high resolution protein structures from the Protein Data Bank suggests that the ADC model is the most accurate and the AES eliminate about half of the incorrectly counted contact pairs when this model is compared to the ISS model.

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“…As this number varies between positions along the sequence, adaptable knowledge-based multibody potentials might be a way forward [35][36][37]. Efforts to model protein structures beyond pairwise formalisms include vectorial representations [38], combining sequence and contact information [39], and other multi-body models [40,41].…”

Section: Essential Subnetworkmentioning

confidence: 99%