scholarly journals k-Best Solutions under Distance Constraints in Valuated ▵-Matroids

1999 ◽  
Vol 22 (4) ◽  
pp. 381-412 ◽  
Author(s):  
Ingo Althöfer ◽  
Walter Wenzel
Keyword(s):  
Distance Constraints ◽  
Valuated Matroids

Statistical Force-Field for Structural Modeling Using Chemical Cross-Linking/mass Spectrometry Distance Constraints

2018 ◽  
Author(s):  
Allan J. R. Ferrari ◽  
Fabio C. Gozzo ◽  
Leandro Martinez
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Force Field ◽  
Protein Structures ◽  
Protein Structure Determination ◽  
Structural Modeling ◽  
Cross Linking ◽  
Amino Acid Residues ◽  
Distance Constraints ◽  
Chemical Cross Linking

<div><p>Chemical cross-linking/Mass Spectrometry (XLMS) is an experimental method to obtain distance constraints between amino acid residues, which can be applied to structural modeling of tertiary and quaternary biomolecular structures. These constraints provide, in principle, only upper limits to the distance between amino acid residues along the surface of the biomolecule. In practice, attempts to use of XLMS constraints for tertiary protein structure determination have not been widely successful. This indicates the need of specifically designed strategies for the representation of these constraints within modeling algorithms. Here, a force-field designed to represent XLMS-derived constraints is proposed. The potential energy functions are obtained by computing, in the database of known protein structures, the probability of satisfaction of a topological cross-linking distance as a function of the Euclidean distance between amino acid residues. The force-field can be easily incorporated into current modeling methods and software. In this work, the force-field was implemented within the Rosetta ab initio relax protocol. We show a significant improvement in the quality of the models obtained relative to current strategies for constraint representation. This force-field contributes to the long-desired goal of obtaining the tertiary structures of proteins using XLMS data. Force-field parameters and usage instructions are freely available at http://m3g.iqm.unicamp.br/topolink/xlff <br></p></div><p></p><p></p>

Structural Complementarity of Distance Constraints Obtained from Chemical Crosslinking and Amino Acid Coevolution

2019 ◽  
Author(s):  
Ricardo N. dos Santos ◽  
F&aacute;bio C. Gozzo ◽  
Faruck Morcos ◽  
Leandro Martinez
Keyword(s):  
Amino Acid ◽  
Chemical Crosslinking ◽  
Distance Constraints

scholarly journals Effects of longitudinal short-distance constraints on the hadronic light-by-light contribution to the muon $$\mathbf {g-2}$$

2020 ◽  
Vol 80 (12) ◽  
Author(s):  
Jan Lüdtke ◽  
Massimiliano Procura
Keyword(s):  
Short Distance ◽  
Independent Method ◽  
Recent Model ◽  
Low Energy ◽  
Muon Anomalous Magnetic Moment ◽  
Distance Constraints ◽  
Independent Information ◽  
Intermediate States ◽  
Model Independent ◽  
Interpolation Functions

AbstractWe present a model-independent method to estimate the effects of short-distance constraints (SDCs) on the hadronic light-by-light contribution to the muon anomalous magnetic moment $$a_\mu ^\text {HLbL}$$ a μ HLbL . The relevant loop integral is evaluated using multi-parameter families of interpolation functions, which satisfy by construction all constraints derived from general principles and smoothly connect the low-energy region with those where either two or all three independent photon virtualities become large. In agreement with other recent model-based analyses, we find that the SDCs and thus the infinite towers of heavy intermediate states that are responsible for saturating them have a rather small effect on $$a_\mu ^\text {HLbL}$$ a μ HLbL . Taking as input the known ground-state pseudoscalar pole contributions, we obtain that the longitudinal SDCs increase $$a_\mu ^\text {HLbL}$$ a μ HLbL by $$(9.1\pm 5.0) \times 10^{-11}$$ ( 9.1 ± 5.0 ) × 10 - 11 , where the isovector channel is responsible for $$(2.6\pm 1.5) \times 10^{-11}$$ ( 2.6 ± 1.5 ) × 10 - 11 . More precise estimates can be obtained with our method as soon as further accurate, model-independent information about important low-energy contributions from hadronic states with masses up to 1–2 GeV become available.

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