A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Filters
GOR Method for Protein Structure Prediction using Cluster Analysis
2013
International Journal of Computer Applications
Preserved Fulltext
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
2002
BMC Genomics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2017
Journal of Molecular Graphics and Modelling
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2007
BMC Structural Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2006
Genome Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2006
Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2008; you can also visit the original URL.
The file type is application/pdf.
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]
2019
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2007
Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2012; you can also visit the original URL.
The file type is application/pdf.
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
2008
The FEBS Journal
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2007
Nature Precedings
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2007
Chinese Physics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2022
PLoS ONE
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
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
1997
Proteins: Structure, Function, and Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2004; you can also visit the original URL.
The file type is application/pdf.
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
1997
Proteins: Structure, Function, and Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2004; you can also visit the original URL.
The file type is application/pdf.
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
2007
Current Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
« Previous
Showing results 1 — 15 out of 2,094 results