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Consensus alignment server for reliable comparative modeling with distant templates

J. C. Prasad, S. Vajda, C. J. Camacho
2004 Nucleic Acids Research  
Consensus is a server developed to produce highquality alignments for comparative modeling, and to identify the alignment regions reliable for copying from a given template.  ...  Combining the output from five different alignment methods, the server produces a consensus alignment, with a reliability measure indicated for each position and a prediction of the regions suitable for  ...  The final output of the server includes the selected consensus with reliable regions identified (Figure 1 ), and the corresponding models of the full consensus alignment and of the reliable regions predicted  ... 
doi:10.1093/nar/gkh456 pmid:15215349 pmcid:PMC441594 fatcat:2ta6pxrtj5dhnmzwusuxpe2ave

PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliability

Mindaugas Margelevicius, Ceslovas Venclovas
2005 BMC Bioinformatics  
PSI-BLAST-ISS is an effective reliability assessment tool that can be useful in applications such as comparative modelling or analysis of individual sequence regions.  ...  It favorably compares with the existing similar software both in the performance and functional features.  ...  The performance of PSI-BLAST-ISS in alignment reliability estimation was directly compared with the Consensus server.  ... 
doi:10.1186/1471-2105-6-185 pmid:16033659 pmcid:PMC1187875 fatcat:tq4jzgstxbclhldfqwieml62se

Comparative modeling in CASP6 using consensus approach to template selection, sequence-structure alignment, and structure assessment

Česlovas Venclovas, Mindaugas Margelevičius
2005 Proteins: Structure, Function, and Bioinformatics  
Likewise, the consensus of multiple alignment variants (or lack of it) was used to initially delineate reliable and unreliable alignment regions.  ...  Along with over 150 other groups we have tested our template-based protein structure prediction approach by submitting models for 30 target proteins to the sixth round of the Critical Assessment of Protein  ...  ACKNOWLEDGMENTS We thank CASP6 organizers and assessors for their hard work, and experimentalists for providing their protein structures.  ... 
doi:10.1002/prot.20725 pmid:16187350 fatcat:kli7eyt6vrdg7ev76fg766vdpe

Methods for Sequence–Structure Alignment [chapter]

Česlovas Venclovas
2011 Msphere  
Hence, a homology model of a protein can be derived using related protein structure(s) as modeling template(s).  ...  A key step in this approach is the establishment of correspondence between residues of the protein to be modeled and those of modeling template(s).  ...  Acknowledgments Ana Vencloviené and members of Venclovas' lab are gratefully acknowledged for useful comments and suggestions.  ... 
doi:10.1007/978-1-61779-588-6_3 pmid:22323217 fatcat:fvv6qwx3lrh2lbmgy55ejmre6q

Pcons.net: protein structure prediction meta server

B. Wallner, P. Larsson, A. Elofsson
2007 Nucleic Acids Research  
The results from these servers are analyzed and assessed for structural correctness using Pcons and ProQ; and the user is presented with a ranked list of possible models.  ...  The Pcons.net Meta Server (http://pcons.net) provides improved automated tools for protein structure prediction and analysis using consensus.  ...  Finding the best possible template. 2. Aligning the template to the query sequence. 3. Building a 3D structure based on the alignment. 4 . Assessing the quality of the model.  ... 
doi:10.1093/nar/gkm319 pmid:17584798 pmcid:PMC1933226 fatcat:pu2ovy6zxndrhkwx66fcjm7sva

Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10

Yang Zhang
2013 Proteins: Structure, Function, and Bioinformatics  
Compared with the traditional threading assembly refinement procedures, the inclusion of the threading-constrained ab initio folding models can consistently improve the quality of the full-length models  ...  We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I-TASSER and QUARK for both free-modeling (FM) and template-based modeling (TBM) targets.  ...  D Xu, J Yang, A Roy, and R Yan for assistance in CASP10.  ... 
doi:10.1002/prot.24341 pmid:23760925 pmcid:PMC4067246 fatcat:eqwxvvjkh5ap7cchhugr2de7ne

Protein structure prediction in 2002

Jack Schonbrun, William J Wedemeyer, David Baker
2002 Current Opinion in Structural Biology  
Acknowledgements We thank Leszek Rychlewski for Table 1  ...  The answer appears to be 'no'; comparative modeling is still limited by the accuracy of the target/template alignments.  ...  The target and template sequences are aligned, and a three-dimensional structure of the target protein is generated from the coordinates of the aligned residues of the template protein, combined with models  ... 
doi:10.1016/s0959-440x(02)00336-6 pmid:12127454 fatcat:4loy6dwerva3fhr5bjcunny5fq

FFAS03: a server for profile-profile sequence alignments

L. Jaroszewski, L. Rychlewski, Z. Li, W. Li, A. Godzik
2005 Nucleic Acids Research  
The server provides access to the alignment analysis, multiple alignment, and comparative modeling tools. Access to the server is open for both academic and commercial researchers.  ...  It is also used by several fold-recognition consensus methods and meta-servers.  ...  and help in maintaining and development of the server and the method.  ... 
doi:10.1093/nar/gki418 pmid:15980471 pmcid:PMC1160179 fatcat:dp7kkda3cvhahatzohczfcjeku

Servers for protein structure prediction

Daniel Fischer
2006 Current Opinion in Structural Biology  
Servers for close and distant homology modeling are now routinely used by many biologists, and have already been applied to the experimental structure determination process itself, and to the interpretation  ...  Because dozens of servers are currently available, it is hard for a biologist to know which server(s) to use; however, the state of the art of these methods is now assessed through the LiveBench and CAFASP  ...  Close and distant homology modeling servers accept a protein's amino acid sequence as input, search known 3D structures for appropriate template(s) and automatically generate a 3D model containing the  ... 
doi:10.1016/j.sbi.2006.03.004 pmid:16546376 fatcat:5jceg2fdg5c5joneabirotj7mi

GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions

Junsu Ko, Hahnbeom Park, Chaok Seok
2012 BMC Bioinformatics  
For application to multi-domain proteins, GalaxyTBM must be combined with domain-splitting methods.  ...  The accuracy of the initial core modeling is enhanced by focusing on more conserved regions in the multiple-template selection and multiple sequence alignment stages.  ...  average GDT-TS of 68.1, compared to 68.4 for Seok-server).  ... 
doi:10.1186/1471-2105-13-198 pmid:22883815 pmcid:PMC3462707 fatcat:3oop27rsgfbabml4vctmbv4xsq

LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins

2019 Nucleic Acids Research  
where LOMETS2 detected 176% more templates with TM-scores >0.5 than the previous LOMETS server for Hard targets that lacked homologous templates.  ...  on distant-homology template identification.  ...  For the full-length model construction, however, the consensus distance restraints collected from multiple complementary template alignments from different threading programs help MODELLER construct much  ... 
doi:10.1093/nar/gkz384 pmid:31081035 pmcid:PMC6602514 fatcat:4xzeqfsqgncwrlxepe3stwo3ou

Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection

Dylan Chivian, David Baker
2006 Nucleic Acids Research  
The accuracy of a homology model based on the structure of a distant relative or other topologically equivalent protein is primarily limited by the quality of the alignment.  ...  The method serves as the foundation of the homology modeling module in the Robetta server.  ...  We additionally appreciate Guoli Wang and Roland Dunbrack for their provision of the CE alignments of the SCOP domains.  ... 
doi:10.1093/nar/gkl480 pmid:16971460 pmcid:PMC1635247 fatcat:s4p75exjqvaf7c4bcefwj7rubq

Non-Linear and Misleading Template Scoring Criteria: Root Cause of Protein Modelling Inaccuracies

Ashish Runthala
2015 Current Synthetic and Systems Biology  
A more reliable and robust scoring measure is thus mandatorily required to select the best possible available template for constructing the most accurate target conformation.  ...  Template based protein modelling is currently the most accurate as well as trustworthy method for predicting the correct protein conformations to bridge the constantly increasing gap between the number  ...  CASP Server models are therefore usually pretty poor topology predictions and are not highly accurate compared to the well justified human models.  ... 
doi:10.4172/2332-0737.1000121 fatcat:e7sflo526zfyllyg2tjoolavqi

Multiple mapping method: A novel approach to the sequence-to-structure alignment problem in comparative protein structure modeling

Brajesh K. Rai, András Fiser
2006 Proteins: Structure, Function, and Bioinformatics  
A major bottleneck in comparative protein structure modeling is the quality of input alignment between the target sequence and the template structure.  ...  In all cases MMM showed statistically significant improvement by reducing alignment errors in the range of 3 to 17%. MMM also compared favorably over two alignment meta-servers.  ...  Eduardo Fajardo, Dmitrij Rykunov, and Narcis Fernandez-Fuentes for their comments on the manuscript, and to Mr. Carlos Madrid for setting up the MMM server.  ... 
doi:10.1002/prot.20835 pmid:16437570 fatcat:26lnpcaefravtlwbav7hd67nv4

Practical lessons from protein structure prediction

K. Ginalski
2005 Nucleic Acids Research  
remain unknown for many protein families.  ...  Alternative cheap and fast methods to assign folds using prediction algorithms continue to provide valuable structural information for many proteins.  ...  ACKNOWLEDGEMENTS The authors would like to express their cordial thanks to the structure prediction community for supporting the evaluation effort and inspiring the progress in the prediction field.  ... 
doi:10.1093/nar/gki327 pmid:15805122 pmcid:PMC1074308 fatcat:bztr5c2h5fb75akxurtcqnqjke
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