Comparison of systematic search and database methods for constructing segments of protein structure
Abstract
Two principal methods of determining the conformation of short pieces of polypeptide backbone in proteins have been developed: using a database of known structures and systematically generating all conformations. In this paper, we compare the effectiveness of these two techniques. The completeness of the database for segments of different lengths is examined and it is found to contain most conformations for segments seven residues long, but to deteriorate rapidly for longer regions. When the database segment is to be incorporated into the rest of a structure, at least seven residues are required to build four new residues, because of the need to position the segment relative to the rest of the structure. It is found that such positioning using flanking residues results in large errors in the inserted region. We conclude that the database method is currently not effective for comparative modeling, even for short segments. The systematic search procedure is found to generate almost all structures of short segments found in proteins. In contrast to the database method, low root mean square error structures are obtained for a set of trial segments embedded in the rest of a protein structure. Thus, it should be considered the method of choice.
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Local conformational restraints greatly reduce the size of the conformational space.
“Local conformational restraints also greatly reduce the size of the space45.”
From Critical assessment of methods of protein structure prediction (CASP)—Round <scp>XIV</scp> (2021) · cites this paper as [45]
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Webb, B., & Šali, A. (2016) · Current Protocols in Bioinformatics · doi:10.1002/cpbi.3 · Cited by 4,349 · see citing works
“…database methods are limited because the number of possible conformations increases exponentially with the length of a loop, and until the late 1990s only loops up to 7 residues long could be modeled using the database of known protein structures (Fidelis et al., 1994; Lessel and Schomburg, 1994).”
Comparative Protein Structure Modeling of Genes and Genomes
Martí-Renom, M. A., Stuart, A. C., Fiser, A., Sánchez, R., Melo, F., & Šali, A. (2000) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.29.1.291 · Cited by 3,169 · see citing works
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BackgroundComparative Protein Structure Modeling Using MODELLER
Eswar, N., Webb, B., Martı́-Renom, M. A., Madhusudhan, M. S., Eramian, D., Shen, M., Pieper, U., & Šali, A. (2007) · Current Protocols in Protein Science · doi:10.1002/0471140864.ps0209s50 · Cited by 2,862 · see citing works
“Correspondingly, the average model accuracy increased from 43% to 54% (the model accuracy was measured as the percentage of the C α atoms of the model that were within 5 ◦ A of the corresponding C α atoms in the superimposed native structure).”
BackgroundModeling of loops in protein structures
Fiser, A., Do, R. K. G., & Šali, A. (2000) · Protein Science · doi:10.1110/ps.9.9.1753 · Cited by 2,116 · see citing works
Modeller: Generation and Refinement of Homology-Based Protein Structure Models
Fiser, A., & Šali, A. (2003) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(03)74020-8 · Cited by 1,684 · see citing works
Simons, K. T., Kooperberg, C. L., Huang, E. S., & Baker, D. A. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.0959 · Cited by 1,387 · see citing works
“Fidelis et al. (1994) suggested that building structures from fragments was likely to be unsuccessful because of the structural divergence of local fragments and the weakness of local sequence-structural correlation.”
BackgroundComparative Protein Structure Modeling Using MODELLER
Webb, B., & Šali, A. (2014) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi0506s47 · Cited by 1,141 · see citing works
Evaluation of comparative protein modeling by M ODELLER
Šali, A., Potterton, L., Feng, Y., van Vlijmen, H., & Karplus, M. (1995) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340230306 · Cited by 1,083 · see citing works
Zhou, H., & Zhou, Y. (2002) · Protein Science · doi:10.1110/ps.0217002 · Cited by 902 · see citing works
“Another multiple decoy set is loops (Moult and James 1986; Fidelis et al. 1994) from http://prostar.”
BackgroundComparative protein modeling by satisfaction of spatial restraints
⩽ali, A. (1995) · Molecular Medicine Today · doi:10.1016/s1357-4310(95)91170-7 · Cited by 785 · see citing works
Comparative protein structure modeling using MODELLER
Webb, B., & Sali, A. (2016) · Current Protocols in Protein Science · doi:10.1002/cpps.20 · Cited by 730 · see citing works
“…database methods are limited because the number of possible conformations increases exponentially with the length of a loop, and until the late 1990s only loops up to 7 residues long could be modeled using the database of known protein structures (Fidelis et al., 1994; Lessel and Schomburg, 1994).”
BackgroundCritical assessment of methods of protein structure prediction (CASP)—Round <scp>XIV</scp>
Kryshtafovych, A., Schwede, T., Topf, M., Fidelis, K., & Moult, J. (2021) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26237 · Cited by 503 · see citing works
“Local conformational restraints also greatly reduce the size of the space.(45) More concrete evidence for this conclusion is provided by the large number of designed proteins that have now been made, with no explicit design of a pathway.”
BackgroundSelf-citationAdvances in Homology Protein Structure Modeling
Xiang, Z. (2006) · Current Protein and Peptide Science · doi:10.2174/138920306777452312 · Cited by 479 · see citing works
Samudrala, R., & Moult, J. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1479 · Cited by 446 · see citing works
“This decoy set consists of sets of conformations for short loops (four or ®ve residues) that were systematically generated using the methods of Moult & James (1986) and Fidelis et al. (1994).”
BackgroundMethodInfluentialSelf-citationXiang, Z., Soto, C. S., & Honig, B. H. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.102179699 · Cited by 368 · see citing works
Advances in comparative protein-structure modelling
Sánchez, R., & Šali, A. (1997) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(97)80027-9 · Cited by 330 · see citing works
Modeling structurally variable regions in homologous proteins with rosetta
Rohl, C. A., Strauss, C. E. M., Chivian, D. C., & Baker, D. A. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10629 · Cited by 321 · see citing works
“…to the SVR following optimal superposition of these stem residues. mations for protein segments up to about five or six residues are adequately sampled in known protein structures, 47 and fragment assembly is unlikely to significantly improve the accuracy of predictions for segments below this size.”
BackgroundAl‐Lazikani, B., Jung, J., Xiang, Z., & Honig, B. H. (2001) · Current Opinion in Chemical Biology · doi:10.1016/s1367-5931(00)00164-2 · Cited by 319 · see citing works
Template-Based Protein Structure Modeling
Fiser, A. (2010) · Methods in molecular biology · doi:10.1007/978-1-60761-842-3_6 · Cited by 264 · see citing works
FREAD revisited: accurate loop structure prediction using a database search algorithm
Choi, Y., & Deane, C. M. (2010) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22658 · Cited by 161 · see citing works
“…The predictive power of database search methods has been questioned and ab initio loop prediction has been thought to be more effective.25 ,26 A recent benchmark27 of four commercial modeling protocols for loop structure prediction (two ab initio : MODELLER11 and PRIME—a commercial…”
MethodPDB-based protein loop prediction: parameters for selection and methods for optimization
van Vlijmen, H., & Karplus, M. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0857 · Cited by 161 · see citing works
“Fidelis et al. (1994) conclude that database searches are limited to loops of four residues.”
BackgroundMethodResultInfluential3D‐SHOTGUN: A novel, cooperative, fold‐recognition meta‐predictor
Fischer, D. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10357 · Cited by 161 · see citing works
“18–20,31, and 32).”
Modelling mutations and homologous proteins
Šali, A. (1995) · Current Opinion in Biotechnology · doi:10.1016/0958-1669(95)80074-3 · Cited by 160 · see citing works
A graph-theoretic algorithm for comparative modeling of protein structure
Samudrala, R., & Moult, J. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.1689 · Cited by 157 · see citing works
“Limitations in accuracy are partly imposed by the loop main-chain sampling of the data base method (Fidelis et al., 1994).”
BackgroundSelf-citationCODA: A combined algorithm for predicting the structurally variable regions of protein models
Deane, C. M., & Blundell, T. L. (2001) · Protein Science · doi:10.1110/ps.37601 · Cited by 151 · see citing works
“As has been argued by Martin et al. (1989), the different methods used in the literature for superposition can give rise to divergent calculations of rmsd (Fidelis et al. 1994), and these are very seldom specified in publications.”
MethodInfluentialde Bakker, P. I. W., DePristo, M. A., Burke, D. F., & Blundell, T. L. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10235 · Cited by 143 · see citing works
DePristo, M. A., de Bakker, P. I. W., Lovell, S. C., & Blundell, T. L. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10285 · Cited by 140 · see citing works
Comparative Protein Structure Modelling
Fiser, A. (2008) · Springer eBooks · doi:10.1007/978-1-4020-9058-5_3 · Cited by 133 · see citing works
Evolution and Physics in Comparative Protein Structure Modeling
Fiser, A., Feig, M., Brooks, C. L., & Šali, A. (2002) · Accounts of Chemical Research · doi:10.1021/ar010061h · Cited by 102 · see citing works
The H3 loop of antibodies shows unique structural characteristics
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Comparative Protein Structure Modeling and its Applications to Drug Discovery
Jacobson, M. P., & Šali, A. (2004) · Annual reports in medicinal chemistry · doi:10.1016/s0065-7743(04)39020-2 · Cited by 97 · see citing works
Wojcik, J., Mornon, J., & Chomilier, J. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.2826 · Cited by 98 · see citing works
Koehl, P., & Delarue, M. H. (1995) · Nature Structural & Molecular Biology · doi:10.1038/nsb0295-163 · Cited by 96 · see citing works
Oliva, B., Bates, P. A., Querol, E., Avilés, F. X., & Sternberg, M. J. E. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.1847 · Cited by 83 · see citing works
Inverse Kinematics in Biology: The Protein Loop Closure Problem
Kolodny, R., Guibas, L., Levitt, M., et al. (2005) · The International Journal of Robotics Research · doi:10.1177/0278364905050352 · Cited by 82 · see citing works
“However, Fidelis et al. (1994) concluded that the use of segments from the PDB was useful only for loops up to a length of four residues, as the completeness of the database degrades rapidly with increasing length.”
BackgroundMethodPredicting protein three-dimensional structure
Moult, J. (1999) · Current Opinion in Biotechnology · doi:10.1016/s0958-1669(99)00037-3 · Cited by 82 · see citing works
Self-citationOPUS‐Ca: A knowledge‐based potential function requiring only Cα positions
Wu, Y., Lu, M., Chen, M., Li, J., & Ma, J. (2007) · Protein Science · doi:10.1110/ps.072796107 · Cited by 80 · see citing works
“The procedure was based on the observation that main chain conformation can be mostly determined by local conformation of C a atoms (Fidelis et al. 1994; Milik et al. 1997).”
MethodA supersecondary structure library and search algorithm for modeling loops in protein structures
Fernandez-Fuentes, N. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl156 · Cited by 76 · see citing works
Protein structure modeling in the proteomics era
Fiser, A. (2004) · Expert Review of Proteomics · doi:10.1586/14789450.1.1.97 · Cited by 70 · see citing works
A divide and conquer approach to fast loop modeling
Tosatto, S. C. E., Bindewald, E., Hesser, J., et al. (2002) · Protein Engineering Design and Selection · doi:10.1093/protein/15.4.279 · Cited by 68 · see citing works
“Combinatorial approaches have been studied by several groups (Moult and James, 1986; Bruccoleri et al., 1988; Brower et al., 1993; Bruccoleri, 1993; Fidelis et al., 1994; Pedersen and Moult, 1995; Deane and Blundell, 2000).”
BackgroundReconstruction of Protein Backbones from the BriX Collection of Canonical Protein Fragments
Baeten, L., Reumers, J., Tur, V., Stricher, F., Lenaerts, T., Serrano, L. G., Rousseau, F., & Schymkowitz, J. W. H. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000083 · Cited by 64 · see citing works
“In previous studies [40,45] loop structures were considered as seven-residue fragments with less than four continuous a-helical or b-strand residues as defined by DSSP.”
BackgroundZolese, G., Falcioni, G., Bertoli, E., Galeazzi, R., Woźniak, M., Wypych, Z., Gratton, E., & Ambrosini, A. (2000) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(20000701)40:1 · Cited by 99 · see citing works
High‐resolution prediction of protein helix positions and orientations
Li, X., Jacobson, M. P., & Friesner, R. A. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20014 · Cited by 60 · see citing works
New approaches in molecular structure prediction
Böhm, G. (1996) · Biophysical Chemistry · doi:10.1016/0301-4622(95)00120-4 · Cited by 60 · see citing works
Modeling Structures and Motions of Loops in Protein Molecules
Shehu, A., & Kavraki, L. E. (2012) · Entropy · doi:10.3390/e14020252 · Cited by 55 · see citing works
A Guide to Template Based Structure Prediction
Qu, X., Swanson, R., Day, R., & Tsai, J. W. (2009) · Current Protein and Peptide Science · doi:10.2174/138920309788452182 · Cited by 47 · see citing works
Local structure prediction with local structure-based sequence profiles
Yang, A., & Wang, L.-Y. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg151 · Cited by 44 · see citing works
“…work on protein structure prediction has shown that local structure predictions are useful in predicting protein structures from protein sequences (Baldwin and Rose, 1999; Bonneau et al., 2001; Fidelis et al., 1994; Rooman et al., 1991; Simon et al., 1991; Unger et al., 1989; Yang and Wang, 2002).”
BackgroundSaturating representation of loop conformational fragments in structure databanks.
Fernández‐Fuentes, N., & Fiser, A. (2006) · BMC Structural Biology · doi:10.1186/1472-6807-6-15 · Cited by 43 · see citing works
“It was concluded that only segments of 7 residues or less (4 loop and 1+2 anchor residues) had most of their conceivable conformations present in the database of known protein structures[11].”
InfluentialOn the properties and sequence context of structurally ambivalent fragments in proteins
Kuznetsov, I. B., & Rackovsky, S. R. (2003) · Protein Science · doi:10.1110/ps.03209703 · Cited by 43 · see citing works
“…is consistent with a previous conclusion that sequence fragments greater than size 7 are not well represented in the database of known structures, and there is no prospect for obtaining a large enough database to adequately represent fragments longer than eight residues (Fidelis et al. 1994).”
BackgroundResultModeling protein loops using a ϕi+1, Ψi dimer database
Sudarsanam, S., DuBose, R. F., March, C. J., & Srinivasan, S. (1995) · Protein Science · doi:10.1002/pro.5560040715 · Cited by 43 · see citing works
Protein fragment clustering and canonical local shapes
Hunter, C. G., & Subramaniam, S. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10309 · Cited by 40 · see citing works
“particular, what is important is how well the database represents the conformational space of local shapes.(18)”
BackgroundMishra, S. K., Saxena, A., & Sangwan, R. S. (2013) · Science International · doi:10.17311/sciintl.2013.237.252 · Cited by 38 · see citing works
Westhead, D. R., & Thornton, J. M. (1998) · Current Opinion in Biotechnology · doi:10.1016/s0958-1669(98)80012-8 · Cited by 38 · see citing works
Improved protein loop prediction from sequence alone
Burke, D. F., & Deane, C. M. (2001) · Protein Engineering Design and Selection · doi:10.1093/protein/14.7.473 · Cited by 37 · see citing works
“As has been noted before (Fidelis et al., 1994; Wojcik et al., 1999), comparison of the accuracy of any loop prediction method with other loop prediction methods is sometimes complicated by the fact that different atoms are used to calculate the final r.m.s.d. of the loop.”
ResultDocking macromolecules with flexible segments
Bastard, K., Thureau, A., Lavery, R., et al. (2003) · Journal of Computational Chemistry · doi:10.1002/jcc.10329 · Cited by 34 · see citing works
Church, W. B., JONES, K. A., Kuiper, D. A., Shine, J., & Iismaa, T. P. (2002) · Protein Engineering Design and Selection · doi:10.1093/protein/15.4.313 · Cited by 33 · see citing works
“…of variable regions in proteins: first, random generation of loop atoms in torsional space (Fine et al., 1986), and second, the ‘fitting’ of protein fragments of known structure and appropriate length on to the flanking elements of secondary structure (Jones and Thirup, 1986; Fidelis et al., 1994).”
BackgroundKuznetsov, I. B., & Rackovsky, S. R. (2004) · Protein Science · doi:10.1110/ps.04833404 · Cited by 32 · see citing works
“Fragments of length five to six are also well represented in the PDB and cover most conformations accessible to a given fragment (Fidelis et al. 1994).”
BackgroundContreras‐Moreira, B., Fitzjohn, P. W., & Bates, P. A. (2002) · PubMed · Cited by 32 · see citing works
Exhaustive docking of molecular fragments with electrostatic solvation
Majeux, N., Scarsi, M., Apostolakis, J., Ehrhardt, C., & Caflisch, A. (1999) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(19991001)37:1 · Cited by 175 · see citing works
Protein local structure prediction from sequence
Hunter, C. G., & Subramaniam, S. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10310 · Cited by 29 · see citing works
A Historical Perspective of Template-Based Protein Structure Prediction
Guo, J.-T., Ellrott, K., & Xu, Y. (2008) · Humana Press eBooks · doi:10.1007/978-1-59745-574-9_1 · Cited by 28 · see citing works
Hvidsten, T. R., Kryshtafovych, A., Komorowski, J., et al. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth062 · Cited by 28 · see citing works
Self-citationMethods for Protein Homology Modelling
Pitman, M. R., & Menz, R. I. (2006) · Applied mycology and biotechnology · doi:10.1016/s1874-5334(06)80005-5 · Cited by 27 · see citing works
Full cyclic coordinate descent: solving the protein loop closure problem in Cα space
Boomsma, W., & Hamelryck, T. (2005) · BMC Bioinformatics · doi:10.1186/1471-2105-6-159 · Cited by 26 · see citing works
Computational challenges in structural and functional genomics
Head-Gordon, T. L., & Wooley, J. (2001) · IBM Systems Journal · doi:10.1147/sj.402.0265 · Cited by 26 · see citing works
Critical Features of Fragment Libraries for Protein Structure Prediction
Trevizani, R., Custódio, F. L., Santos, K. B., et al. (2017) · PLoS ONE · doi:10.1371/journal.pone.0170131 · Cited by 24 · see citing works
Discrete restraint‐based protein modeling and the Cα‐trace problem
DePristo, M. A., de Bakker, P. I. W., Shetty, R. P., et al. (2003) · Protein Science · doi:10.1110/ps.0386903 · Cited by 23 · see citing works
“For knowledge-based methods, the coverage of fragments extracted from the database of proteins can be a source of model inaccuracy on unusual conformations, such as loops that exhibit substantial structural variability (Fidelis et al. 1994).”
MethodStructural Conservation in Single-Domain Proteins: Implications for Homology Modeling
D'Alfonso, G., Tramontano, A. L., & Lahm, A. (2001) · Journal of Structural Biology · doi:10.1006/jsbi.2001.4351 · Cited by 23 · see citing works
“There are also procedures that are the combination of both ( Fidelis et al., 1994; van Vlijmen and Karplus, 1997)”
BackgroundOptimization of solvation models for predicting the structure of surface loops in proteins
Das, B., & Meirovitch, H. (2001) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.1041 · Cited by 23 · see citing works
A quality metric for homology modeling: the H-factor
di Luccio, E., & Koehl, P. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-48 · Cited by 23 · see citing works
Das, B., & Meirovitch, H. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10356 · Cited by 22 · see citing works
Comparative protein structure modeling as an optimization problem
Sánchez, R., & Šali, A. (1997) · Journal of Molecular Structure THEOCHEM · doi:10.1016/s0166-1280(96)04971-8 · Cited by 22 · see citing works
Confronting the problem of interconnected structural changes in the comparative modeling of proteins
Samudrala, R., Pedersen, J. T., Zhou, H., et al. (1995) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340230307 · Cited by 22 · see citing works
Self-citationFernández‐Fuentes, N., Querol, E., Avilés, F. X., et al. (2005) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20516 · Cited by 21 · see citing works
“…of the fragment to be compared (there are different superposition methods described in the literature that can give different RMSD values 21 ); (2) selected atoms to calculate the final RMSD (i.e., main-chain atom only or main-chain plus side-chain atoms, etc.); and (3) design of the…”
BackgroundMethodCarugo, O., & Argos, P. (1998) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(19980501)31:2 · Cited by 72 · see citing works
Janardhan, A. H., & Vajda, S. (1998) · Protein Science · doi:10.1002/pro.5560070812 · Cited by 21 · see citing works
Hvidsten, T. R., Kryshtafovych, A., & Fidelis, K. A. (2008) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22296 · Cited by 20 · see citing works
Self-citationBates, P. A., Dokurno, P., Freemont, P. S., & Sternberg, M. J. E. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.2210 · Cited by 20 · see citing works
Structure prediction for the helical skeletons detected from the low resolution protein density map
Nasr, K. A., Sun, W., & He, J. J. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-s1-s44 · Cited by 17 · see citing works
“Once the structure of the skeletons are predicted, loops can be added using our previous method [12][13] or other existing loop closure methods [14-20].”
MethodSiew, N., & Fischer, D. (2001) · IBM Systems Journal · doi:10.1147/sj.402.0410 · Cited by 17 · see citing works
Abagyan, R. A., Batalov, S., Cardozo, T. J., Totrov, M. M., Webber, J., & Zhou, Y. (1997) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(1997)1+ · Cited by 78 · see citing works
Designing succinct structural alphabets
Li, S. C., Bu, D., Gao, X. D., et al. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn165 · Cited by 16 · see citing works
Comparative Protein Structure Modeling
Fiser, A., Sánchez, R., Melo, F., & Fiser, A. (2001) · CRC Press eBooks · doi:10.1201/9780203903827.pt3 · Cited by 18 · see citing works
A Modular Perspective of Protein Structures: Application to Fragment Based Loop Modeling
Fernández‐Fuentes, N., & Fiser, A. (2012) · Methods in molecular biology · doi:10.1007/978-1-62703-065-6_9 · Cited by 13 · see citing works
“Similarly to the prediction of protein structures there are ab initio (conformational search) methods (40–42), and database search (or knowledge-based) methods (43–45).”
MethodNasr, K. A., & He, J. J. (2009) · International Journal of Data Mining and Bioinformatics · doi:10.1504/ijdmb.2009.026712 · Cited by 13 · see citing works
“These conformations are then refined to satisfy the anchors (Fidelis et al., 1994; Li et al., 1999; Vlijmen and Karplus, 1997; Wojcik et al., 1999).”
BackgroundComparative Modeling of Drug Target Proteins☆
Webb, B., Eswar, N., Fan, H., Khuri, N., Pieper, U., Dong, G., & Šali, A. (2014) · Elsevier eBooks · doi:10.1016/b978-0-12-409547-2.11133-3 · Cited by 13 · see citing works
Clinciu, D. L., Chen, Y., Ko, C.-N., et al. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-s4-s26 · Cited by 13 · see citing works
“In addition, GEMDOCK has been successfully applied to identify inhibitors and binding sites for some targets [23-27].”
Exploring the conformational diversity of loops on conserved frameworks
Li, W., Liang, S., Wang, R., et al. (1999) · Protein Engineering Design and Selection · doi:10.1093/protein/12.12.1075 · Cited by 13 · see citing works
Computing Protein Structures from Electron Density Maps: The Missing Fragment Problem
Lotan, I., van den Bedem, H., Deacon, A. M., et al. (2005) · Springer tracts in advanced robotics · doi:10.1007/10991541_24 · Cited by 12 · see citing works
“The applicability of this approach was initially limited to loops of length 4 [26], but later work suggested an upper limit of 9 [61].”
BackgroundAb initio construction of all-atom loop conformations
Jiang, H., & Blouin, C. (2005) · Journal of Molecular Modeling · doi:10.1007/s00894-005-0030-x · Cited by 12 · see citing works
Detecting local residue environment similarity for recognizing near‐native structure models
Kim, H., & Kihara, D. (2014) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24658 · Cited by 11 · see citing works
Computational Modeling of Protein Three-Dimensional Structure: Methods and Resources
Pan, A., Gnanasekar, P., & Chakraborty, S. S. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-822312-3.00023-0 · Cited by 12 · see citing works
Comparative Protein Structure Modelling
Fiser, A. (2017) · Springer eBooks · doi:10.1007/978-94-024-1069-3_4 · Cited by 10 · see citing works
Computational Biochemistry of Antibodies and T-Cell Receptors
Novotný, J., & Bajorath, J. (1996) · Advances in protein chemistry · doi:10.1016/s0065-3233(08)60490-8 · Cited by 10 · see citing works
Clustering and percolation in protein loop structures
Peng, X., He, J., & Niemi, A. J. (2015) · BMC Structural Biology · doi:10.1186/s12900-015-0049-x · Cited by 8 · see citing works
“The success in loop modelling is also often limited to super-secondary structures where α -helices and β -strands are connected to each other by relatively short twists and turns [16, 17].”
BackgroundModeling Protein Structure from its Sequence
Martı́-Renom, M. A., Madhusudhan, M. S., Eswar, N., Pieper, U., Shen, M., Šali, A., Fiser, A., Mirković, N., John, B., & Stuart, A. C. (2003) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi0501s03 · Cited by 9 · see citing works
“Even according to the more optimistic estimate, ∼30% and 60% of all the possible 8 and 9 residue loop conformations, respectively, are missing from the database (Fidelis et al., 1994).”
BackgroundModeling Loops in Protein Structures
Fernández‐Fuentes, N., & Fiser, A. (2010) · doi:10.1002/9780470882207.ch13 · Cited by 8 · see citing works
3.13 Computational Methods Related to Molecular Structure and Reaction Chemistry of Biomaterials ☆
Farokhirad, S., Bradley, R. P., Sarkar, A., Shih, A., Telesco, S., Liu, Y., Venkatramani, R., Eckmann, D. M., AYYASWAMY, P. S., & Radhakrishnan, R. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-803581-8.10216-4 · Cited by 7 · see citing works
- Authors
- Fidelis, K., Stern, P. S., Bacon, D., & Moult, J.
- Affiliations
- University of Maryland Biotechnology Institute (US)
- Venue
- "Protein Engineering, Design and Selection"
- Publisher
- Oxford University Press (OUP)
- Published
- 1994
- Volume
- 7
- Issue
- 8
- Pages
- 953-960
- ISSN
- 0269-2139 (ISSN-L)
- 1741-0126
- 1741-0134
- OpenAlex
- W1990698302
- Cited by
- 126
- References
- 0
- Citations by year
- 2025: 1 · 2021: 2 · 2017: 4 · 2016: 2 · 2015: 1 · 2014: 4 · 2013: 1 · 2012: 4
- FWCI
- 2.02
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Protein Engineering Design and Selection (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health (5r01lm005102-03, 5r01gm041034-10)
- National Institute of General Medical Sciences (GM41034)
- U.S. National Library of Medicine (LM05102)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
- Keywords
- protein structure comparison, conformational space, structure database, comparative protein modeling, root mean square error
- MeSH terms
- Computer Simulation, Models, Molecular, Peptide Fragments, Databases, Factual, Sequence Alignment, Protein Structure, Secondary
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