FREAD revisited: Accurate loop structure prediction using a database search algorithm

2009 ◽  
Vol 78 (6) ◽  
pp. 1431-1440 ◽  
Author(s):  
Yoonjoo Choi ◽  
Charlotte M. Deane
Keyword(s):  
Structure Prediction ◽  
Search Algorithm ◽  
Database Search ◽  
Loop Structure

OPTIMAL DATABASE SEARCH: WAVES AND CATALYSIS

2006 ◽  
Vol 04 (05) ◽  
pp. 815-825 ◽  
Author(s):  
APOORVA PATEL
Keyword(s):  
Quantum Computation ◽  
Search Algorithm ◽  
Database Search ◽  
Harmonic Oscillators ◽  
Physical Realization ◽  
Classical Wave ◽  
Superposition Of States

Grover's database search algorithm, although discovered in the context of quantum computation, can be implemented using any system that allows superposition of states. A physical realization of this algorithm is described using coupled simple harmonic oscillators, which can be exactly solved in both classical and quantum domains. Classical wave algorithms are far more stable against decoherence compared to their quantum counterparts. In addition to providing convenient demonstration models, they may have a role in practical situations, such as catalysis.

scholarly journals A hierarchical MS2 /MS3 database search algorithm for automated analysis of phosphopeptide tandem mass spectra

PROTEOMICS ◽  
2009 ◽  
Vol 9 (7) ◽  
pp. 1763-1770 ◽  
Author(s):  
Hua Xu ◽  
Liwen Wang ◽  
Larry Sallans ◽  
Michael A. Freitas
Keyword(s):  
Mass Spectra ◽  
Search Algorithm ◽  
Automated Analysis ◽  
Database Search ◽  
Tandem Mass ◽  
Tandem Mass Spectra

Protein Loop Structure Prediction Using Conformational Space Annealing

2017 ◽  
Vol 57 (5) ◽  
pp. 1068-1078 ◽  
Author(s):  
Seungryong Heo ◽  
Juyong Lee ◽  
Keehyoung Joo ◽  
Hang-Cheol Shin ◽  
Jooyoung Lee
Keyword(s):  
Structure Prediction ◽  
Conformational Space ◽  
Loop Structure

Protein Loop Structure Prediction Methods

2008 ◽  
pp. 3100-3105
Author(s):  
Martin Mönnigmann ◽  
Christodoulos A. Floudas
Keyword(s):  
Structure Prediction ◽  
Prediction Methods ◽  
Loop Structure

Smotifs as structural local descriptors of supersecondary elements: classification, completeness and applications

2014 ◽  
Vol 10 (4) ◽  
Author(s):  
Jaume Bonet ◽  
Andras Fiser ◽  
Baldo Oliva ◽  
Narcis Fernandez-Fuentes
Keyword(s):  
Protein Design ◽  
Structure Prediction ◽  
Protein Structures ◽  
Regular Structure ◽  
Loop Structure ◽  
Apparent Lack ◽  
Knowledge Based ◽  
Limits Of Knowledge ◽  
Folding Dynamics ◽  
And Function

AbstractProtein structures are made up of periodic and aperiodic structural elements (i.e., α-helices, β-strands and loops). Despite the apparent lack of regular structure, loops have specific conformations and play a central role in the folding, dynamics, and function of proteins. In this article, we reviewed our previous works in the study of protein loops as local supersecondary structural motifs or Smotifs. We reexamined our works about the structural classification of loops (ArchDB) and its application to loop structure prediction (ArchPRED), including the assessment of the limits of knowledge-based loop structure prediction methods. We finalized this article by focusing on the modular nature of proteins and how the concept of Smotifs provides a convenient and practical approach to decompose proteins into strings of concatenated Smotifs and how can this be used in computational protein design and protein structure prediction.

scholarly journals QUANTUM ORACLES IN TERMS OF UNIVERSAL GATE SET

2011 ◽  
Vol 09 (06) ◽  
pp. 1363-1381 ◽  
Author(s):  
YUJI TANAKA ◽  
TSUBASA ICHIKAWA ◽  
MASAHITO TADA-UMEZAKI ◽  
YUKIHIRO OTA ◽  
MIKIO NAKAHARA
Keyword(s):  
Arbitrary Number ◽  
Search Algorithm ◽  
Circuit Complexity ◽  
Database Search ◽  
Quantum Circuits ◽  
Systematic Construction ◽  
Universal Gate

We present a systematic construction of quantum circuits implementing Grover's database search algorithm for arbitrary number of targets. We introduce a new operator which flips the sign of the targets and evaluate its circuit complexity. We find the condition under which the circuit complexity of the database search algorithm based on this operator is less than that of the conventional one.

scholarly journals Structure prediction of crystals, surfaces and nanoparticles

2020 ◽  
Vol 378 (2186) ◽  
pp. 20190600
Author(s):  
Scott M. Woodley ◽  
Graeme M. Day ◽  
R. Catlow
Keyword(s):  
Machine Learning ◽  
Energy Function ◽  
Structure Prediction ◽  
Search Algorithm ◽  
Structure And Function ◽  
Current Status ◽  
Organic Systems ◽  
And Function

We review the current techniques used in the prediction of crystal structures and their surfaces and of the structures of nanoparticles. The main classes of search algorithm and energy function are summarized, and we discuss the growing role of methods based on machine learning. We illustrate the current status of the field with examples taken from metallic, inorganic and organic systems. This article is part of a discussion meeting issue ‘Dynamic in situ microscopy relating structure and function’.

pFind–Alioth: A novel unrestricted database search algorithm to improve the interpretation of high-resolution MS/MS data

2015 ◽  
Vol 125 ◽  
pp. 89-97 ◽  
Author(s):  
Hao Chi ◽  
Kun He ◽  
Bing Yang ◽  
Zhen Chen ◽  
Rui-Xiang Sun ◽  
...  
Keyword(s):  
High Resolution ◽  
Search Algorithm ◽  
Database Search
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