Using least median of squares for structural superposition of flexible proteins

Liu, Yu Shen; Fang, Yi; Ramani, Karthik

doi:10.1186/1471-2105-10-29

Cited by 18 publications

(26 citation statements)

References 47 publications

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“…Although there are several approaches to address this problem,57–60 we developed a robust statistical approach to automatically determine the appropriate transformation matrix, while simultaneously being aware of flexible and rigid parts within the protein. Our implementation is a modification of the wRMSD algorithm,61 where the superposition errors are Gaussian weighted so that residues that move the least have greater weighting andin turn dominate the computation of rigid body parameters.…”

Section: Methodsmentioning

confidence: 99%

Event detection and sub‐state discovery from biomolecular simulations using higher‐order statistics: Application to enzyme adenylate kinase

Ramanathan¹,

Savol²,

Agarwal³

et al. 2012

Proteins

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Biomolecular simulations at milli-second and longer timescales can provide vital insights into functional mechanisms. Since post-simulation analyses of such large trajectory data-sets can be a limiting factor in obtaining biological insights, there is an emerging need to identify key dynamical events and relating these events to the biological function online, that is, as simulations are progressing. Recently, we have introduced a novel computational technique, quasi-anharmonic analysis (QAA) (PLoS One 6(1): e15827), for partitioning the conformational landscape into a hierarchy of functionally relevant sub-states. The unique capabilities of QAA are enabled by exploiting anharmonicity in the form of fourth-order statistics for characterizing atomic fluctuations. In this paper, we extend QAA for analyzing long time-scale simulations online. In particular, we present HOST4MD - a higher-order statistical toolbox for molecular dynamics simulations, which (1) identifies key dynamical events as simulations are in progress, (2) explores potential sub-states and (3) identifies conformational transitions that enable the protein to access those sub-states. We demonstrate HOST4MD on micro-second time-scale simulations of the enzyme adenylate kinase in its apo state. HOST4MD identifies several conformational events in these simulations, revealing how the intrinsic coupling between the three sub-domains (LID, CORE and NMP) changes during the simulations. Further, it also identifies an inherent asymmetry in the opening/closing of the two binding sites. We anticipate HOST4MD will provide a powerful and extensible framework for detecting biophysically relevant conformational coordinates from long time-scale simulations.

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Section: Methodsmentioning

confidence: 99%

Event detection and sub‐state discovery from biomolecular simulations using higher‐order statistics: Application to enzyme adenylate kinase

Ramanathan¹,

Savol²,

Agarwal³

et al. 2012

Proteins

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“…The second category of approaches is based on structure analysis methods, which are generally used in protein structure analysis. Specially, if given a pair of protein structures [7,11,14], the junctions are often found through structure alignment between the two proteins. If only an individual protein structure is given without referring to any other proteins [19,20], junction prediction usually takes advantage of some additional chemical information of the protein itself, such as amino acid sequences.…”

Section: Junction Detection For 3d Shapesmentioning

confidence: 99%

“…Note that a class of junction detection methods (e.g. [7,11,14]) is based on shape alignment/comparison techniques, which first compare two or more different shapes and then determine the correspondences and junctions. Unlike the comparison-based techniques, our method only resorts to the geometric representation of the given individual shape.…”

Section: Introductionmentioning

confidence: 99%

VIV: Using visible internal volume to compute junction-aware shape descriptor of 3D articulated models

et al. 2016

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An articulated shape is composed of a set of rigid parts connected by some flexible junctions. Junctions have been demonstrated to be critical local features in many visual tasks such as feature recognition, segmentation, matching, motion tracking and functional prediction. However, efficient description and detection of junctions still remain a research challenge due to the high complexity of articulated deformation. This paper presents a novel junctionaware shape descriptor for a 3D articulated model defined by a closed manifold surface. To encode junction information on the shape boundary, the core idea is to develop a new geometric measure, called the visible internal volume (VIV) function, which associates the shape's volumetric context to its boundary surface. The VIV at an arbitrary point on the shape boundary is defined as the volume of visible region within the shape as observed from the point. The VIV variation serves as the new shape descriptor. One advantage of using the VIV for 3D articulated shape description is that it is robust to articulation and it reflects the shape structure and deformation well without any explicit shape decomposition or prior skeleton extraction * procedure. The experimental results and several potential applications are presented for demonstrating the effectiveness of our method.

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“…However, even for this purpose, the best way to overlay the ensemble members to calculate the “average” structure has not been standardized. Overlays are often performed based on all backbone or Cα atoms as well as based on a subset of such atoms from “ordered” residues subjectively defined by casual inspection of the initial overlay based on all atoms . Or one may use a program that more objectively weights atoms to optimize the superimposition.…”

Section: Introductionmentioning

confidence: 99%

“…Overlays are often performed based on all backbone or Ca atoms as well as based on a subset of such atoms from "ordered" residues subjectively defined by casual inspection of the initial overlay based on all atoms. [12][13][14][15] Or one may use a program that more objectively weights atoms to optimize the superimposition. Three of these are: THESEUS, an approach that superimposes structures using all atoms with maximal likelihood derived weights 16 ; CYRANGE, part of the CYANA software package that automatically identifies residue ranges to guide superposition 14 ; and SuperPose, a web server that defines regions to use for superposition by comparing difference distance matrices based on a-carbons.…”

Section: Introductionmentioning

confidence: 99%

Residue‐level global and local ensemble‐ensemble comparisons of protein domains

2015

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Many methods of protein structure generation such as NMR-based solution structure determination and template-based modeling do not produce a single model, but an ensemble of models consistent with the available information. Current strategies for comparing ensembles lose information because they use only a single representative structure. Here, we describe the ENSEM-BLATOR and its novel strategy to directly compare two ensembles containing the same atoms to identify significant global and local backbone differences between them on per-atom and perresidue levels, respectively. The ENSEMBLATOR has four components: eePREP (ee for ensembleensemble), which selects atoms common to all models; eeCORE, which identifies atoms belonging to a cutoff-distance dependent common core; eeGLOBAL, which globally superimposes all models using the defined core atoms and calculates for each atom the two intraensemble variations, the interensemble variation, and the closest approach of members of the two ensembles; and eeLOCAL, which performs a local overlay of each dipeptide and, using a novel measure of local backbone similarity, reports the same four variations as eeGLOBAL. The combination of eeGLOBAL and eeLOCAL analyses identifies the most significant differences between ensembles. We illustrate the ENSEMBLATOR's capabilities by showing how using it to analyze NMR ensembles and to compare NMR ensembles with crystal structures provides novel insights compared to published studies. One of these studies leads us to suggest that a "consistency check" of NMR-derived ensembles may be a useful analysis step for NMR-based structure determinations in general. The ENSEMBLATOR 1.0 is available as a first generation tool to carry out ensemble-ensemble comparisons.

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Using least median of squares for structural superposition of flexible proteins

Cited by 18 publications

References 47 publications

Event detection and sub‐state discovery from biomolecular simulations using higher‐order statistics: Application to enzyme adenylate kinase

Event detection and sub‐state discovery from biomolecular simulations using higher‐order statistics: Application to enzyme adenylate kinase

VIV: Using visible internal volume to compute junction-aware shape descriptor of 3D articulated models

Residue‐level global and local ensemble‐ensemble comparisons of protein domains

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