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Protein structure search and local structure characterization

Shih-Yen Ku, Yuh-Jyh Hu
2008 BMC Bioinformatics  
First, we wanted to introduce a modular design pipeline to those who have been working with structural alphabets.  ...  Structural alphabets allow us to characterize local structures of proteins and describe the global folding structure of a protein using a one-dimensional (1D) sequence.  ...  Acknowledgements Thanks go to Jinn-Moon Yang and Chi-Hua Tung for their assistance in using 3D-BLAST.  ... 
doi:10.1186/1471-2105-9-349 pmid:18721472 pmcid:PMC2529324 fatcat:24d73movkjfobex473mz3r2l6u

Use of a structural alphabet to find compatible folds for amino acid sequences

Swapnil Mahajan, Alexandre G. de Brevern, Yves-Henri Sanejouand, Narayanaswamy Srinivasan, Bernard Offmann
2014 Protein Science  
We propose an original method that computes the conditional probabilities for the amino-acid sequence of a protein to fit to known protein 3D structures using a structural alphabet, known as "Protein Blocks  ...  It is used to encode 3D protein structures into 1D PB sequences and to capture sequence to structure relationships.  ...  Results The general objective of this work is to investigate how a structural alphabet can be used to identify the compatible folds for a set of protein sequences with unknown structure.  ... 
doi:10.1002/pro.2581 pmid:25297700 pmcid:PMC4282420 fatcat:zr2ndng5mjgvrf642girpxamru

An alphabetic code based atomic level molecular similarity search in databases

Saranya Nallusamy, Samuel Selvaraj
2012 Bioinformation  
The main goal of structure-based drug design (SBDD) is to find novel lead compounds with potent and specific activity.  ...  Thus, a common pattern was extracted using this set of compounds for database searching to retrieve similar active compounds.  ...  Acknowledgement: We thank University Grants Commission, New Delhi for the award of RGNFS fellowship to N.S.  ... 
doi:10.6026/97320630008498 pmid:22829718 pmcid:PMC3398777 fatcat:mxdvu2ha7jcsvmezwvkva4p7de

Introduction to the Rosetta Special Collection

Sagar D. Khare, Timothy A. Whitehead, Yang Zhang
2015 PLoS ONE  
A Rosetta Conference (RosettaCon) describing updates to the Rosetta source code is held annually.  ...  The Rosetta macromolecular modeling software is a versatile, rapidly developing set of tools that are now being routinely utilized to address state-of-the-art research challenges in academia and industrial  ...  Protein Multispecificity Design The design of multi-specificity of proteins is important in applications ranging from structural vaccine design, bispecific antibody therapy, and combinatorial biocatalysis  ... 
doi:10.1371/journal.pone.0144326 pmid:26714017 pmcid:PMC4700992 fatcat:7eyke4jnlzebjmbghe5oeypmma

iPBA: a tool for protein structure comparison using sequence alignment strategies

Jean-Christophe Gelly, Agnel Praveen Joseph, Narayanaswamy Srinivasan, Alexandre G. de Brevern
2011 Nucleic Acids Research  
Protein Blocks (PBs) is a widely used structural alphabet with 16 pentapeptide conformations that can fairly approximate a complete protein chain.  ...  We propose an efficient method for structure comparison, based on a structural alphabet.  ...  ACKNOWLEDGEMENTS The authors would also like to thank the anonymous reviewers for their help in improving the manuscript.  ... 
doi:10.1093/nar/gkr333 pmid:21586582 pmcid:PMC3125758 fatcat:hzpydg2n6vbk5lsi2w4fj64fxi

Toward high-resolution computational design of the structure and function of helical membrane proteins

Patrick Barth, Alessandro Senes
2016 Nature Structural & Molecular Biology  
The emergence of new structural methods for membrane proteins will accelerate progress  ...  The computational design of α-helical membrane proteins is still in its infancy but has made important progress.  ...  Acknowledgments PB was supported by National Institutes of Health Grant R01GM097207, by a Lilly Research Award Program and by a supercomputer allocation from XSEDE (MCB120101).  ... 
doi:10.1038/nsmb.3231 pmid:27273630 pmcid:PMC4962061 fatcat:7zf7fn2plvanlot2jstp6am5ni

Structural alphabets derived from attractors in conformational space

Alessandro Pandini, Arianna Fornili, Jens Kleinjung
2010 BMC Bioinformatics  
The fragments of the Structural Alphabet are equivalent to the conformational attractors and therefore yield a most informative encoding of proteins.  ...  Conclusions: The density-based Structural Alphabet provides a novel tool to describe local conformations and it is specifically suitable for application in studies of protein dynamics.  ...  This suggests the importance of designing strategies to estimate the weight of this inaccuracy in the encoding.  ... 
doi:10.1186/1471-2105-11-97 pmid:20170534 pmcid:PMC2838871 fatcat:rc4sbwm2mndvfehdi7b4pm57xy

Searching for the Pareto frontier in multi-objective protein design

Vikas Nanda, Sandeep V. Belure, Ofer M. Shir
2017 Biophysical Reviews  
The goal of protein engineering and design is to identify sequences that adopt three-dimensional structures of desired function.  ...  We review progress in multi-objective protein design, the development of Pareto optimization methods, and present a specific case study using multiobjective optimization methods to model the tradeoff between  ...  A number of strategies have emerged in the field for dealing with the inherent multi-objective nature of protein design problems.  ... 
doi:10.1007/s12551-017-0288-0 pmid:28799089 pmcid:PMC5578931 fatcat:soldirukyvhlrou7zqg7q7k5sy

A method for computing the inter-residue interaction potentials for reduced amino acid alphabet

Abhinav Luthra, Anupam Nath Jha, G. K. Ananthasuresh, Saraswathi Vishveswara
2007 Journal of Biosciences  
This can be valuable in designing the protein structures.  ...  Hence, it is desirable to reduce the alphabet of 20 amino acids to a smaller number.  ...  Acknowledgments The help of Mr Sourav Rakshit in writing the computer program that was used to create the MDS map is gratefully acknowledged.  ... 
doi:10.1007/s12038-007-0088-y pmid:17914230 fatcat:rdh4gdkwyvbvxgwpa5ngiindbq

NMRDSP: An Accurate Prediction of Protein Shape Strings from NMR Chemical Shifts and Sequence Data

Wusong Mao, Peisheng Cong, Zhiheng Wang, Longjian Lu, Zhongliang Zhu, Tonghua Li, Lukasz Kurgan
2013 PLoS ONE  
Nuclear magnetic resonance chemical shifts give a strong correlation with the local protein structure, and are exploited to predict protein structures in conjunction with computational approaches.  ...  We have constructed the NMRDSP web server and believe it could be employed to provide a solid platform to predict other protein structures and functions. The NMRDSP web server is freely available at  ...  Selecting effective features is the key for successfully designing a protein structural sequence predictor.  ... 
doi:10.1371/journal.pone.0083532 pmid:24376713 pmcid:PMC3871590 fatcat:2fankard5je6lkicqbf4mhqazu

A genetic approach for building different alphabets for peptide and protein classification

Loris Nanni, Alessandra Lumini
2008 BMC Bioinformatics  
Conclusion: The validity of the novel strategy for creating reduced alphabets is demonstrated by the performance improvement obtained by the proposed approach with respect to other reduced alphabets-based  ...  In this paper, it is proposed an optimization approach for producing reduced alphabets for peptide classification, using a Genetic Algorithm.  ...  Acknowledgements The authors would like to thank: I. Bozic for sharing the Vaccine datasets; L. Huang for sharing the Peptide dataset; T. Rögnvaldsson for sharing the HIV1 dataset, A.  ... 
doi:10.1186/1471-2105-9-45 pmid:18218100 pmcid:PMC2246158 fatcat:dm7qqelsyzbmlis6ingl53ku2m

Improved Large-Scale Homology Search by Two-Step Seed Search Using Multiple Reduced Amino Acid Alphabets

Kazuki Takabatake, Kazuki Izawa, Motohiro Akikawa, Keisuke Yanagisawa, Masahito Ohue, Yutaka Akiyama
2021 Genes  
In this paper, we propose a new, high-performance homology search algorithm that employs a two-step seed search strategy using multiple reduced amino acid alphabets to identify highly similar subsequences  ...  Metagenomic analysis, a technique used to comprehensively analyze microorganisms present in the environment, requires performing high-precision homology searches on large amounts of sequencing data, the  ...  This is called a seed search strategy. RAPSearch2, GHOSTZ, and DIAMOND achieve highly efficient and accurate searches by employing reduced amino acid alphabets in their seed search strategies.  ... 
doi:10.3390/genes12091455 pmid:34573438 pmcid:PMC8469100 fatcat:neohyzn6bngpxdu53va3vm3rhy

BOSS: Bayesian Optimization over String Spaces [article]

Henry B. Moss, Daniel Beck, Javier Gonzalez, David S. Leslie, Paul Rayson
2020 arXiv   pre-print
Experiments demonstrate considerably improved optimization over existing approaches across a broad range of constraints, including the popular setting where syntax is governed by a context-free grammar  ...  Recent applications of BO over strings have been hindered by the need to map inputs into a smooth and unconstrained latent space. Learning this projection is computationally and data-intensive.  ...  Acknowledgments The authors are grateful to reviewers, whose comments and advice have improved this paper.  ... 
arXiv:2010.00979v1 fatcat:dryufghyzrgc7f2jt6sf3b35yu

Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit

2019 Bioinformatics  
It can be used to incorporate sequence annotations, such as secondary structure or (DNA) motifs, into the alignment scoring, as well as to customize many other aspects of a progressive multiple alignment  ...  PRALINE 2 is a toolkit for custom multiple sequence alignment workflows.  ...  To this end PRALINE 2 was designed around a component architecture.  ... 
doi:10.1093/bioinformatics/btz572 pmid:31368486 pmcid:PMC6954659 fatcat:piru5evktjdkhdtmp5d4rvbucy

A Comparative View Of Applying Linear And Non-Linear Visualisation Approaches To Protein Dataset

Saba Manzoor, Fawwad Jaskani, Omer Riaz
2018 EAI Endorsed Transactions on Creative Technologies  
Consensus sequence of data was checked later, the purpose of this sequence is to check the occurrence of each alphabet in a column.  ...  The alphabet that was maximum was converted to binary code 1 and remaining were converted to 0. When the data was converted in to binary then models were applied on the data.  ...  Multi-Dimensional Scaling MDS MDS is the accumulation of non-direct strategies to change the high dimensional data into low dimensional data.  ... 
doi:10.4108/eai.13-7-2018.161109 fatcat:zvgjbh64mnhxrlhza7zsd3w7ei
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