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MA Lomize, AL Lomize, ID Pogozheva, HI Mosberg (2006)
OPM: Orientations of Proteins in Membranes databaseBioinformatics, 22
A Camproux, R Gautier, P Tuffery (2004)
A Hidden Markov Model Derived Structural Alphabet for ProteinsJ. Mol. Biol., 339
W Dyrka, AT Augousti, M Kotulska (2008)
Ion flux through membrane channels–an enhanced algorithm for the Poisson-Nernst-Planck modelJ Comput Chem, 29
JP Ebejer, JR Hill, S Kelm, J Shi, CM Deane (2013)
Memoir: template-based structure prediction for membrane proteinsNucleic Acids Res, 41
JM Duarte, R Sathyapriya, H Stehr, I Filippis, M Lappe (2010)
Optimal contact definition for reconstruction of contact mapsBMC Bioinformatics, 11
P Tuffery, F Guyon, P Derreumaux (2005)
Improved Greedy Algorithm for Protein Structure ReconstructionJ Comp Chem, 26
M Vendruscolo, E Kussell, E Domany (1997)
Recovery of protein structure from contact mapsFold Des, 2
W Dyrka, MM Bartuzel, M Kotulska (2013)
Optimization of 3D Poisson-Nernst-Planck model for fast evaluation of diverse protein channelsProteins, 81
TF Havel, ID Kuntz, GM Crippen (1983)
The combinatorial distance geometry method for the calculation of molecular conformation. I. A new approach to an old problemJ Theor Biol, 104
MS Jafri, M Kotulska (2006)
Modeling the mechanism of metabolic oscillations in ischemic cardiac myocytesJ Theor Biol, 242
(Maupetit J, Gautier R, Tuffery P (2006) SABBAC: online Structural Alphabet-based protein Back Bone reconstruction from Alpha-Carbon trace. Nucl Acids Res 34 (Web Server issue):W147–W151)
Maupetit J, Gautier R, Tuffery P (2006) SABBAC: online Structural Alphabet-based protein Back Bone reconstruction from Alpha-Carbon trace. Nucl Acids Res 34 (Web Server issue):W147–W151Maupetit J, Gautier R, Tuffery P (2006) SABBAC: online Structural Alphabet-based protein Back Bone reconstruction from Alpha-Carbon trace. Nucl Acids Res 34 (Web Server issue):W147–W151, Maupetit J, Gautier R, Tuffery P (2006) SABBAC: online Structural Alphabet-based protein Back Bone reconstruction from Alpha-Carbon trace. Nucl Acids Res 34 (Web Server issue):W147–W151
DE Kim, F Dimaio, R Yu-Ruei Wang, Y Song, D Baker (2014)
One contact for every twelve residues allows robust and accurate topology-level protein structure modelingProteins, 82
T Nugent, DT Jones (2012)
Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysisProc Natl Acad Sci U S A, 109
R Sathyapriya, JM Duarte, H Stehr, I Filippis, M Lappe (2009)
Defining an Essence of Structure Determining Residue Contacts in ProteinsPLoS Comput Biol, 5
(Kryshtafovych A, Fidelis K, Moult J (2013) CASP10 results compared to those of previous CASP experiments. Proteins, “Accepted Article”, Proteins 82 Suppl 2:164-74. doi: 10.1002/prot.24448)
Kryshtafovych A, Fidelis K, Moult J (2013) CASP10 results compared to those of previous CASP experiments. Proteins, “Accepted Article”, Proteins 82 Suppl 2:164-74. doi: 10.1002/prot.24448Kryshtafovych A, Fidelis K, Moult J (2013) CASP10 results compared to those of previous CASP experiments. Proteins, “Accepted Article”, Proteins 82 Suppl 2:164-74. doi: 10.1002/prot.24448, Kryshtafovych A, Fidelis K, Moult J (2013) CASP10 results compared to those of previous CASP experiments. Proteins, “Accepted Article”, Proteins 82 Suppl 2:164-74. doi: 10.1002/prot.24448
K Arnold, L Bordoli, J Kopp, T Schwede (2006)
The SWISS-MODEL Workspace: A web-based environment for protein structure homology modellingBioinformatics, 22
WR Taylor, DT Jones, MI Sadowski (2012)
Protein topology from predicted residue contactsProtein Sci, 21
DS Marks, LJ Colwell, R Sheridan, TA Hopf, A Pagnani (2011)
Protein 3D Structure Computed from Evolutionary Sequence VariationPLoS ONE, 6
HK Ho, MJ Kuiper, R Kotagiri (2008)
PConPy–a Python module for generating 2D protein mapsBioinformatics, 24
(Söding J, Biegert A, Lupas AN (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 33(Web Server issue):W244–8)
Söding J, Biegert A, Lupas AN (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 33(Web Server issue):W244–8Söding J, Biegert A, Lupas AN (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 33(Web Server issue):W244–8, Söding J, Biegert A, Lupas AN (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 33(Web Server issue):W244–8
HM Berman, J Westbrook, Z Feng, G Gilliland, TN Bhat, H Weissig, IN Shindyalov, PE Bourne (2000)
The Protein Data BankNucl. Acids Res, 28
B Monastyrskyy, K Fidelis, A Tramontano, A Kryshtafovych (2011)
Evaluation of residue–residue contact predictions in CASP9Proteins, 79
J Söding, A Biegert, AN Lupas (2005)
The HHpred interactive server for protein homology detection and structure predictionNucleic Acids Res, 33
M Källberg, H Wang, S Wang, J Peng, Z Wang, HXuJ Lu (2012)
Template-based protein structure modeling using the RaptorX web serverNature Protocols, 7
TJ Taylor, H Bai, CH Tai, B Lee (2014)
Assessment of CASP10 contact-assisted predictionsProteins, 82
(Duarte JM, Sathyapriya R, Stehr H, Filippis I, Lappe M (2010b) RECONSTRUCT - Protein contact map reconstruction using the TINKER package, http://www.bioinformatics.org/owl/reconstruct/index.html)
Duarte JM, Sathyapriya R, Stehr H, Filippis I, Lappe M (2010b) RECONSTRUCT - Protein contact map reconstruction using the TINKER package, http://www.bioinformatics.org/owl/reconstruct/index.htmlDuarte JM, Sathyapriya R, Stehr H, Filippis I, Lappe M (2010b) RECONSTRUCT - Protein contact map reconstruction using the TINKER package, http://www.bioinformatics.org/owl/reconstruct/index.html, Duarte JM, Sathyapriya R, Stehr H, Filippis I, Lappe M (2010b) RECONSTRUCT - Protein contact map reconstruction using the TINKER package, http://www.bioinformatics.org/owl/reconstruct/index.html
NA Baker, D Sept, S Joseph, MJ Holst, JA McCammon (2001)
Electrostatics of nanosystems: application to microtubules and the ribosomeProc. Natl. Acad. Sci., 98
DT Jones, DW Buchan, D Cozzetto, M Pontil (2012)
PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignmentsBioinformatics, 28
GG Krivov, MV Shapovalov, RL Dunbrack (2009)
Improved prediction of protein side–chain conformations with SCWRL4Proteins, 77
(Kozma D, Simon I, Tusnády GE (2012) PDBTM: Protein Data Bank of transmembrane proteins after 8 years. Nucleic Acids Research 33 Database Issue: D275-D278)
Kozma D, Simon I, Tusnády GE (2012) PDBTM: Protein Data Bank of transmembrane proteins after 8 years. Nucleic Acids Research 33 Database Issue: D275-D278Kozma D, Simon I, Tusnády GE (2012) PDBTM: Protein Data Bank of transmembrane proteins after 8 years. Nucleic Acids Research 33 Database Issue: D275-D278, Kozma D, Simon I, Tusnády GE (2012) PDBTM: Protein Data Bank of transmembrane proteins after 8 years. Nucleic Acids Research 33 Database Issue: D275-D278
M Vassura, L Margara, P Lena, F Medri, P Fariselli, R Casadio (2008)
FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact mapsBioinformatics, 24
TA Hopf, LJ Colwell, R Sheridan, B Rost, C Sander, DS Marks (2012)
Three-dimensional structures of membrane proteins from genomic sequencingCell, 149
LA Kelley, MJE Sternberg (2009)
Protein structure prediction on the web: a case study using the Phyre serverNat Protoc, 4
Knowledge of the three-dimensional structures of ion channels allows for modeling their conductivity characteristics using biophysical models and can lead to discovering their cellular functionality. Recent studies show that quality of structure predictions can be significantly improved using protein contact site information. Therefore, a number of procedures for protein structure prediction based on their contact-map have been proposed. Their comparison is difficult due to different methodologies used for validation. In this work, a Contact Map-to-Structure pipeline (C2S_pipeline) for contact-based protein structure reconstruction is designed and validated. The C2S_pipeline can be used to reconstruct monomeric and multimeric proteins. The median RMSD of structures obtained during validation on a representative set of protein structures, equaled 5.27 Å, and the best structure was reconstructed with RMSD of 1.59 Å. The validation is followed by a detailed case study on the KcsA ion channel. Models of KcsA are reconstructed based on different portions of contact site information. Structural feature analysis of acquired KcsA models is supported by a thorough analysis of electrostatic potential distributions inside the channels. The study shows that electrostatic parameters are correlated with structural quality of models. Therefore, they can be used to discriminate between high and low quality structures. We show that 30 % of contact information is needed to obtain accurate structures of KcsA, if contacts are selected randomly. This number increases to 70 % in case of erroneous maps in which the remaining contacts or non-contacts are changed to the opposite. Furthermore, the study reveals that local reconstruction accuracy is correlated with the number of contacts in which amino acid are involved. This results in higher reconstruction accuracy in the structure core than peripheral regions.
The Journal of Membrane Biology – Springer Journals
Published: Mar 29, 2014
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