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GOR Method for Protein Structure Prediction using Cluster Analysis

Rajbir singh, Neha Jain, Dheeraj Pal Kaur
2013 International Journal of Computer Applications  
GOR method uses the information theory to generate the code that relates amino acids sequence and secondary structure of proteins.  ...  The problem of this research focus on secondary structure prediction of amino acids.  ...  Alpha helix: Alpha helix is most commonly known as 4turn helix and it's the commonly occurring type of element in proteins. The helical structure is used to arrange amino acids through 5A wide.  ... 
doi:10.5120/12702-9495 fatcat:hddf7hk6z5cbjklkt4v5w2ycna

Four signature motifs define the first class of structurally related large coiled-coil proteins in plants

Frank Gindullis, Annkatrin Rose, Shalaka Patel, Iris Meier
2002 BMC Genomics  
A homolog sharing the structural features was identified in the monocot rice, indicating conservation among angiosperms.  ...  Filament-like plant proteins (FPP) were identified by sequence similarity to a tomato cDNA that encodes a coiled-coil protein which interacts with the nuclear envelope-associated protein, MAF1.  ...  The secondary structures of the proteins, α-helical, and coiled-coil regions were analyzed using DNASTAR PROTEAN software and the coiled-coil regions were confirmed with the MultiCoil algorithm [2] .  ... 
doi:10.1186/1471-2164-3-9 fatcat:egoba2pvwzf5jmk3rq7tltntpy

Ethanol binding sites on proteins

Vladislav Victorovich Khrustalev, Tatyana Aleksandrovna Khrustaleva, Sergey Vladimirovich Lelevich
2017 Journal of Molecular Graphics and Modelling  
For each amino acid residue found in this way we collected an information on the distribution of other amino acids and the elements of secondary structure (See Supplementary Material Secondary Structure  ...  The preference for being included in alpha helices among amino acids binding ethanol suggested previously [1] is residue-specific.  ... 
doi:10.1016/j.jmgm.2017.10.017 pmid:29078103 fatcat:znomhm5rwzccta3jn3m3f5dgku

A generalized analysis of hydrophobic and loop clusters within globular protein sequences

Richard Eudes, Khanh Le Tuan, Jean Delettré, Jean-Paul Mornon, Isabelle Callebaut
2007 BMC Structural Biology  
Moreover, the analysis of the hydrophobic cluster amino acid composition generally allows for finer prediction of the regular secondary structure associated with the considered cluster within a cluster  ...  Hydrophobic cluster species are predominantly associated with regular secondary structures, and a large part (60 %) reveals preferences for alpha-helices or beta-strands.  ...  Bianco and Alain Soyer for critical reading of the manuscript.  ... 
doi:10.1186/1472-6807-7-2 pmid:17210072 pmcid:PMC1774571 fatcat:euyva7exs5eetffssys2zezymq

A highly divergent gene cluster in honey bees encodes a novel silk family

T. D. Sutherland, P. M. Campbell, S. Weisman, H. E. Trueman, A. Sriskantha, W. J. Wanjura, V. S. Haritos
2006 Genome Research  
We also thank Stephen Trowell for advice on the manuscript, Dennis Anderson for the supply of bees and fascinating discussions on their biology, and John Trueman for invaluable advice and help with alignment  ...  Acknowledgments We thank the Baylor College of Medicine Human Genome Sequencing Center for making the Apis mellifera and Tribolium castaneum gene sequences publicly available before publication.  ...  As the unusual secondary structure and amino acid profile of honey bee silk imply a novel primary silk sequence, we have investigated the silk proteins and genes and their genomic organization.  ... 
doi:10.1101/gr.5052606 pmid:17065612 pmcid:PMC1626643 fatcat:a34r4xjfzzefbiijzb3v7rtuh4

Support vector machines for prediction of dihedral angle regions

O. Zimmermann, U. H. E. Hansmann
2006 Bioinformatics  
Motivation: Most secondary structure prediction programs target only alpha helix and beta sheet structures and summarize all other structures in the random coil pseudo class.  ...  Trained on 20,000 residues our approach leads to dihedral region predictions, that in regions without alpha helices or beta sheets is higher than those from secondary structure prediction programs.  ...  Neumann Institute for Computing in Jülich, Germany.  ... 
doi:10.1093/bioinformatics/btl489 pmid:17005536 fatcat:nd6jw6pypnbbdhojvoqnchhwfm

Artificial intelligence method to design and fold alpha-helix structural proteins from the primary amino acid sequence [article]

Zhao Qin, Lingfei Wu, Hui Sun, Siyu Huo, Tengfei Ma, Eugene Lim, Pin-Yu Chen, Benedetto Marelli, Markus J. Buehler
2019 bioRxiv   pre-print
AbstractWe report an artificial intelligence (AI) based method to predict the molecular structure of proteins, focused here on an important subclass of proteins dominated by alpha-helix secondary structure  ...  The method directly predicts the phi-psi dihedral angles of the backbone of each constituting amino acid, which is then used to construct the full all-atom 3D structure of the corresponding protein without  ...  The authors acknowledge the Center for Materials Science and Engineering (CMSE) and Biophysical Instrumentation Facility (BIF) at MIT for access to the structural characterization and imaging instruments  ... 
doi:10.1101/660639 fatcat:e3skeu5emzdkddftkrycjuimue

Using an alignment of fragment strings for comparing protein structures

I. Friedberg, T. Harder, R. Kolodny, E. Sitbon, Z. Li, A. Godzik
2007 Bioinformatics  
Using KL-strings, we develop an infrastructure for comparing protein structures with a 1D representation. This study focuses on the added value gained from such a description.  ...  similarities when used with a pairwise alignment benchmark.  ...  ACKNOWLEDGEMENTS We are grateful to Barry Grant and Łukasz Jaroszewski for their assistance in analyzing the substitution matrices.  ... 
doi:10.1093/bioinformatics/btl310 pmid:17237095 fatcat:b7ohhxmvufbjlbj57abn27xkk4

Abundance of intrinsic disorder in SV-IV, a multifunctional androgen-dependent protein secreted from rat seminal vesicle

Silvia Vilasi, Raffaele Ragone
2008 The FEBS Journal  
It was inferred that the global structure of SV-IV is not similar to any protein of known three-dimensional structure.  ...  Abbreviations: rat seminal vesicle protein no. 4, SV-IV; intrinsically disordered proteins, IDPs; hydrophobic cluster analysis, HCA; support vector machine, SVM.  ...  In the HCA analysis, the protein sequence is shown on a duplicated α-helical net with hydrophobic clusters identified by solid contours and amino acid numbers indicated on top. , , , and refer to proline  ... 
doi:10.1111/j.1742-4658.2007.06242.x pmid:18215165 fatcat:ylc3kupghrccnlzlncxnbzrzgq

Abundance of intrinsic disorder in SV-IV, a multifunctional androgen-dependent protein secreted from rat seminal vesicle

Silvia Vilasi, Raffaele Ragone
2007 Nature Precedings  
It was inferred that the global structure of SV-IV is not similar to any protein of known three-dimensional structure.  ...  Abbreviations: rat seminal vesicle protein no. 4, SV-IV; intrinsically disordered proteins, IDPs; hydrophobic cluster analysis, HCA; support vector machine, SVM.  ...  In the HCA analysis, the protein sequence is shown on a duplicated α-helical net with hydrophobic clusters identified by solid contours and amino acid numbers indicated on top. , , , and refer to proline  ... 
doi:10.1038/npre.2007.1394.1 fatcat:yjrlypfv5fd2bfwaoutadmqale

Protein structural codes and nucleation sites for protein folding

Jiang Fan, Li Nan
2007 Chinese Physics  
Segments of 17 residues around the top 20% conserved amino acids are analysed, resulting in approximately 100 clusters each for the main secondary structure classes of helix, sheet and coil.  ...  We propose that the central sequences in these clusters form 'structural codes', a useful basis set for identifying nucleation sites, protein fragments stable in isolation, and secondary structural patterns  ...  The mutability measures how easy it is for an amino acid to change to other amino acids with similar structures and properties.  ... 
doi:10.1088/1009-1963/16/2/019 fatcat:6vywtv2hnzdlrah3jmvfgozoiq

Genome-wide exploration of sugar transporter (sweet) family proteins in Fabaceae for Sustainable protein and carbon source

Nisha Singh, Megha Ujinwal, Sapna Langyan, R. Z. Sayyed, Hesham Ali El Enshasy, Ahmed A. Kenawy, Pradeep Kumar
2022 PLoS ONE  
Secondary structure analysis shown that these proteins are richer in alpha-helix (40%) than extended strand (30%) and random coil (25%), respectively.  ...  This study conducted a systematic search for STPs in Cajanus cajan using the Blastp algorithm to understand its molecular basis.  ...  Acknowledgments We acknowledge the Department of Science & Technology (DST INSPIRE), Government of India and RMC, UTM, Malaysia for support.  ... 
doi:10.1371/journal.pone.0268154 pmid:35560044 pmcid:PMC9106169 fatcat:untudrxszvhcbljbarovgrne6u

Patterns, structures, and amino acid frequencies in structural building blocks, a protein secondary structure classification scheme

Jacquelyn S. Fetrow, Michael J. Palumbo, George Berg
1997 Proteins: Structure, Function, and Bioinformatics  
e.g., helix caps and strand caps); 3) strong amino acid preferences are revealed at some positions in some SBBs; and 4) distinct patterns of SBBs occur in the "random coil" regions of proteins.  ...  Analysis of these patterns identifies interesting structural motifs in the protein backbone structure, indicating that SBBs can be used as "building blocks" in the analysis of protein structure.  ...  ACKNOWLEDGMENTS We thank Trevor Creamer and Reggie Aurora for stimulating discussions and useful comments, Chip Lawrence for help with statistics, Alan Grossfield for suggesting the use of Hinton diagrams  ... 
doi:10.1002/(sici)1097-0134(199702)27:2<249::aid-prot11>3.0.co;2-m pmid:9061789 fatcat:n5p4y4pxtfgdjhy5ghtdbyewli

Patterns, structures, and amino acid frequencies in structural building blocks, a protein secondary structure classification scheme

Jacquelyn S. Fetrow, Michael J. Palumbo, George Berg
1997 Proteins: Structure, Function, and Bioinformatics  
e.g., helix caps and strand caps); 3) strong amino acid preferences are revealed at some positions in some SBBs; and 4) distinct patterns of SBBs occur in the "random coil" regions of proteins.  ...  Analysis of these patterns identifies interesting structural motifs in the protein backbone structure, indicating that SBBs can be used as "building blocks" in the analysis of protein structure.  ...  ACKNOWLEDGMENTS We thank Trevor Creamer and Reggie Aurora for stimulating discussions and useful comments, Chip Lawrence for help with statistics, Alan Grossfield for suggesting the use of Hinton diagrams  ... 
doi:10.1002/(sici)1097-0134(199702)27:2<249::aid-prot11>3.3.co;2-x pmid:9061789 fatcat:mgcymmipzjctlobjfwwtgfomby

Local Protein Structures

Bernard Offmann, Manoj Tyagi, Akexandre de Brevern
2007 Current Bioinformatics  
HAL author manuscript inserm-00175058, version 1 Local Protein Structures (Offmann, Tyagi & de Brevern) 3 can result in different lengths for the repetitive structures, depending on the algorithm used.  ...  Protein structures are classically described as composed of two regular states, the αhelices and the β-strands and one non-regular and variable state, the coil.  ...  For each conformational class, amino acid sequence preferences were identified.  ... 
doi:10.2174/157489307781662105 fatcat:wosaroff5jhcnojc7zlozpvd5e
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