Structural modeling of protein complexes: Current capabilities and challenges
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Kliment Olechnovič | Česlovas Venclovas | Justas Dapkūnas | Č. Venclovas | J. Dapkūnas | Kliment Olechnovič
[1] D. Baker,et al. Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information , 2014, eLife.
[2] SödingJohannes. Protein homology detection by HMM--HMM comparison , 2005 .
[3] Torsten Schwede,et al. Assessment of protein assembly prediction in CASP12 , 2018, Proteins.
[4] Anna Tramontano,et al. Evaluation of the template‐based modeling in CASP12 , 2018, Proteins.
[5] Lukas Zimmermann,et al. A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. , 2017, Journal of molecular biology.
[6] Ceslovas Venclovas,et al. The PPI 3 D web server for searching , analyzing and modeling protein – protein interactions in the context of 3 D structures , 2017 .
[7] Kliment Olechnovic,et al. Voronota: A fast and reliable tool for computing the vertices of the Voronoi diagram of atomic balls , 2014, J. Comput. Chem..
[8] Patrick Aloy,et al. Assessing the applicability of template-based protein docking in the twilight zone. , 2014, Structure.
[9] Burkhard Rost,et al. Alternative Protein-Protein Interfaces Are Frequent Exceptions , 2012, PLoS Comput. Biol..
[10] D. Ritchie,et al. Protein docking using spherical polar Fourier correlations , 2000, Proteins.
[11] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[12] Björn Wallner,et al. InterPred: A pipeline to identify and model protein-protein interactions , 2016, bioRxiv.
[13] Zoran Obradovic,et al. Statistical analysis of interface similarity in crystals of homologous proteins. , 2008, Journal of molecular biology.
[14] Adam Zemla,et al. Critical assessment of methods of protein structure prediction (CASP)‐round V , 2005, Proteins.
[15] Yang Zhang,et al. Template-based structure modeling of protein-protein interactions. , 2014, Current opinion in structural biology.
[16] Kliment Olechnovič,et al. Modeling of protein complexes in CAPRI Round 37 using template‐based approach combined with model selection , 2018, Proteins.
[17] Daisuke Kihara,et al. Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment , 2016, Proteins.
[18] Sameer Velankar,et al. The challenge of modeling protein assemblies: the CASP12‐CAPRI experiment , 2018, Proteins.
[19] O. Keskin,et al. Predicting Protein-Protein Interactions from the Molecular to the Proteome Level. , 2016, Chemical reviews.
[20] Carles Pons,et al. pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring , 2013, Bioinform..
[21] Kliment Olechnovic,et al. VoroMQA web server for assessing three-dimensional structures of proteins and protein complexes , 2019, Nucleic Acids Res..
[22] Marco Biasini,et al. lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests , 2013, Bioinform..
[23] Karl Frank,et al. Structure-Based Characterization of Multiprotein Complexes , 2014, Structure.
[24] D. Ritchie,et al. Spherical polar Fourier assembly of protein complexes with arbitrary point group symmetry , 2016 .
[25] Toshiyuki Oda,et al. Template‐based quaternary structure prediction of proteins using enhanced profile–profile alignments , 2017, Proteins.
[26] Raphaël Guérois,et al. PPI4DOCK: large scale assessment of the use of homology models in free docking over more than 1000 realistic targets , 2016, Bioinform..
[27] T. Schwede,et al. Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology , 2017, Scientific Reports.
[28] J. Skolnick,et al. TM-align: a protein structure alignment algorithm based on the TM-score , 2005, Nucleic acids research.
[29] Frank DiMaio,et al. Automatic structure prediction of oligomeric assemblies using Robetta in CASP12 , 2018, Proteins.
[30] Silvio C. E. Tosatto,et al. The Pfam protein families database in 2019 , 2018, Nucleic Acids Res..
[31] Krzysztof Fidelis,et al. Processing and evaluation of predictions in CASP4 , 2001, Proteins.
[32] S. Wodak,et al. Modeling protein–protein and protein–peptide complexes: CAPRI 6th edition , 2017, Proteins.
[33] Kliment Olechnovič,et al. VoroMQA: Assessment of protein structure quality using interatomic contact areas , 2017, Proteins.
[34] Roger Marti,et al. Long tail fibres of the novel broad‐host‐range T‐even bacteriophage S16 specifically recognize Salmonella OmpC , 2013, Molecular microbiology.
[35] The UniProt Consortium,et al. UniProt: a worldwide hub of protein knowledge , 2018, Nucleic Acids Res..
[36] C. E. Peishoff,et al. A critical assessment of docking programs and scoring functions. , 2006, Journal of medicinal chemistry.
[37] Robert D. Finn,et al. HMMER web server: 2018 update , 2018, Nucleic Acids Res..
[38] Guilhem Faure,et al. InterEvScore: a novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution , 2013, Bioinform..
[39] S. Wodak,et al. Assessment of blind predictions of protein–protein interactions: Current status of docking methods , 2003, Proteins.
[40] R. Abagyan,et al. Identification of protein-protein interaction sites from docking energy landscapes. , 2004, Journal of molecular biology.
[41] Jessica Andreani,et al. Lessons from (co‐)evolution in the docking of proteins and peptides for CAPRI Rounds 28–35 , 2017, Proteins.
[42] Thomas A. Hopf,et al. Sequence co-evolution gives 3D contacts and structures of protein complexes , 2014, eLife.
[43] R. Russell,et al. The relationship between sequence and interaction divergence in proteins. , 2003, Journal of molecular biology.
[44] Rohita Sinha,et al. Docking by structural similarity at protein‐protein interfaces , 2010, Proteins.
[45] Ilya A Vakser,et al. Modeling complexes of modeled proteins , 2017, Proteins.
[46] Kliment Olechnovic,et al. The PPI3D web server for searching, analyzing and modeling protein‐protein interactions in the context of 3D structures , 2016, Bioinform..
[47] A. Tramontano,et al. Critical assessment of methods of protein structure prediction (CASP)—Round XII , 2018, Proteins.
[48] K. Henrick,et al. Inference of macromolecular assemblies from crystalline state. , 2007, Journal of molecular biology.
[49] Yang Zhang,et al. Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling. , 2011, Structure.
[50] Thomas L. Madden,et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.
[51] Jose M. Duarte,et al. Automated evaluation of quaternary structures from protein crystals , 2017, bioRxiv.
[52] Kliment Olechnovič,et al. CAD‐score: A new contact area difference‐based function for evaluation of protein structural models , 2013, Proteins.
[53] C Venclovas,et al. Processing and analysis of CASP3 protein structure predictions , 1999, Proteins.
[54] T. Blundell,et al. Comparative protein modelling by satisfaction of spatial restraints. , 1993, Journal of molecular biology.
[55] A. Tramontano,et al. Critical assessment of methods of protein structure prediction (CASP)—round IX , 2011, Proteins.