Caretta – A multiple protein structure alignment and feature extraction suite

Graphical abstract

[1]  P. Hogeweg,et al.  The alignment of sets of sequences and the construction of phyletic trees: An integrated method , 2005, Journal of Molecular Evolution.

[2]  C. Orengo,et al.  One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. , 2002, Journal of molecular biology.

[3]  S. Muggleton,et al.  Modelling the structure and function of enzymes by machine learning. , 1992, Faraday discussions.

[4]  J. Skolnick,et al.  TM-align: a protein structure alignment algorithm based on the TM-score , 2005, Nucleic acids research.

[5]  Benoit H. Dessailly,et al.  Exploring the structure and function paradigm. , 2008, Current opinion in structural biology.

[6]  Eugene I Shakhnovich,et al.  Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[7]  Maksim V Shegay,et al.  parMATT: parallel multiple alignment of protein 3D-structures with translations and twists for distributed-memory systems , 2019, Bioinform..

[8]  Dachuan Zhang,et al.  MMDB and VAST+: tracking structural similarities between macromolecular complexes , 2013, Nucleic Acids Res..

[9]  Ivet Bahar,et al.  ProDy: Protein Dynamics Inferred from Theory and Experiments , 2011, Bioinform..

[10]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[11]  A. Elofsson,et al.  Structure is three to ten times more conserved than sequence—A study of structural response in protein cores , 2009, Proteins.

[12]  Hao Ding,et al.  Similarity-based machine learning methods for predicting drug-target interactions: a brief review , 2014, Briefings Bioinform..

[13]  Bartek Wilczynski,et al.  Biopython: freely available Python tools for computational molecular biology and bioinformatics , 2009, Bioinform..

[14]  Daron M. Standley,et al.  MAFFT-DASH: integrated protein sequence and structural alignment , 2019, Nucleic Acids Res..

[15]  Gert Vriend,et al.  A series of PDB related databases for everyday needs , 2010, Nucleic Acids Res..

[16]  Lenore Cowen,et al.  Matt: Local Flexibility Aids Protein Multiple Structure Alignment , 2008, PLoS Comput. Biol..

[17]  R Nussinov,et al.  Automated multiple structure alignment and detection of a common substructural motif , 2001, Proteins.

[18]  Gaël Varoquaux,et al.  Scikit-learn: Machine Learning in Python , 2011, J. Mach. Learn. Res..

[19]  A. Valencia,et al.  Prediction of protein--protein interaction sites in heterocomplexes with neural networks. , 2002, European journal of biochemistry.

[20]  John P. Overington,et al.  HOMSTRAD: A database of protein structure alignments for homologous families , 1998, Protein science : a publication of the Protein Society.

[21]  W. Kabsch A solution for the best rotation to relate two sets of vectors , 1976 .

[22]  Gert Vriend,et al.  Everyday , 2020, Oxford Research Encyclopedia of Literature.

[23]  A. Konagurthu,et al.  MUSTANG: A multiple structural alignment algorithm , 2006, Proteins.

[24]  Yang Zhang,et al.  mTM‐align: an algorithm for fast and accurate multiple protein structure alignment , 2018, Bioinform..

[25]  Bruno Bauwens,et al.  LZW-Kernel: fast kernel utilizing variable length code blocks from LZW compressors for protein sequence classification , 2018, Bioinform..

[26]  Ruth Nussinov,et al.  MultiProt - A Multiple Protein Structural Alignment Algorithm , 2002, WABI.

[27]  Khaled Rasheed,et al.  Classifying kinase conformations using a machine learning approach , 2017, BMC Bioinformatics.

[28]  D R Flower,et al.  The lipocalin protein family: structural and sequence overview. , 2000, Biochimica et biophysica acta.

[29]  Olivier Poch,et al.  BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations , 2001, Nucleic Acids Res..

[30]  Lode Wyns,et al.  SABmark- a benchmark for sequence alignment that covers the entire known fold space , 2005, Bioinform..

[31]  Philip M. Kim,et al.  Combining Structural Modeling with Ensemble Machine Learning to Accurately Predict Protein Fold Stability and Binding Affinity Effects upon Mutation , 2014, PloS one.

[32]  T. K. Vintsyuk Speech discrimination by dynamic programming , 1968 .

[33]  M. Noble,et al.  Structural characterization of the cyclin-dependent protein kinase family. , 2013, Biochemical Society transactions.

[34]  S. Altschul,et al.  Optimal sequence alignment using affine gap costs. , 1986, Bulletin of mathematical biology.

[35]  Jacques Chomilier,et al.  Protein multiple alignments: sequence-based versus structure-based programs , 2019, Bioinform..

[36]  Enrico Ferraro,et al.  A novel structure-based encoding for machine-learning applied to the inference of SH3 domain specificity , 2006, Bioinform..