Bi-alignments with affine gaps costs

[1]  Gyu Rie Lee,et al.  Accurate prediction of protein structures and interactions using a 3-track neural network , 2021, Science.

[2]  Oriol Vinyals,et al.  Highly accurate protein structure prediction with AlphaFold , 2021, Nature.

[3]  P. Stadler Alignments of biomolecular contact maps , 2021, Interface Focus.

[4]  Peter F. Stadler,et al.  Compositional Properties of Alignments , 2020, Mathematics in Computer Science.

[5]  K. L. Harris,et al.  Structure of an ancestral mammalian family 1B1 cytochrome P450 with increased thermostability , 2020, The Journal of Biological Chemistry.

[6]  Michael T. Wolfinger,et al.  Incongruences Between Sequence and Secondary Structure Alignments of Nucleic Acids , 2020 .

[7]  Peter F. Stadler,et al.  Bi-Alignments as Models of Incongruent Evolution of RNA Sequence and Structure , 2019, bioRxiv.

[8]  Peter F. Stadler,et al.  Bi-alignments as Models of Incongruent Evolution of RNA Sequence and Secondary Structure , 2019, CIBB.

[9]  Bogdan Lesyng,et al.  Theoretical and Computational Aspects of Protein Structural Alignment , 2018, Springer Series on Bio- and Neurosystems.

[10]  Peter F. Stadler,et al.  Alignments as Compositional Structures , 2018, ArXiv.

[11]  Peter F. Stadler,et al.  Partially Local Multi-way Alignments , 2018, Math. Comput. Sci..

[12]  G. Cerqueira,et al.  A mechanism for a single nucleotide intron shift , 2017, Nucleic acids research.

[13]  M. Csűrös,et al.  Splice Sites Seldom Slide: Intron Evolution in Oomycetes , 2016, Genome biology and evolution.

[14]  Peter F. Stadler,et al.  Product Grammars for Alignment and Folding , 2015, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[15]  Günter P. Wagner,et al.  Homology, Genes, and Evolutionary Innovation , 2014 .

[16]  T. Ashok Kumar,et al.  CFSSP: Chou and Fasman Secondary Structure Prediction Server , 2013 .

[17]  Thomas A. Hopf,et al.  Protein structure prediction from sequence variation , 2012, Nature Biotechnology.

[18]  Shuai Cheng Li,et al.  The difficulty of protein structure alignment under the RMSD , 2013, Algorithms for Molecular Biology.

[19]  P. Stadler,et al.  Some novel intron positions in conserved Drosophila genes are caused by intron sliding or tandem duplication , 2010, BMC Evolutionary Biology.

[20]  P. Alexander,et al.  A minimal sequence code for switching protein structure and function , 2009, Proceedings of the National Academy of Sciences.

[21]  Aleksandar Poleksic,et al.  Algorithms for optimal protein structure alignment , 2009, Bioinform..

[22]  Rolf Backofen,et al.  Conserved introns reveal novel transcripts in Drosophila melanogaster. , 2009, Genome research.

[23]  Venky N. Iyer,et al.  Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation , 2008, PLoS genetics.

[24]  Mark P. Styczynski,et al.  BLOSUM62 miscalculations improve search performance , 2008, Nature Biotechnology.

[25]  Peter F Stadler,et al.  Progressive multiple sequence alignments from triplets , 2007, BMC Bioinformatics.

[26]  Reed A. Cartwright,et al.  Logarithmic gap costs decrease alignment accuracy , 2006, BMC Bioinformatics.

[27]  Peter J. Stuckey,et al.  Progressive Multiple Alignment Using Sequence Triplet Optimizations and Three-residue Exchange Costs , 2004, J. Bioinform. Comput. Biol..

[28]  Sean R Eddy,et al.  Where did the BLOSUM62 alignment score matrix come from? , 2004, Nature Biotechnology.

[29]  John D. Kececioglu,et al.  Aligning alignments exactly , 2004, RECOMB.

[30]  Berthold Göttgens,et al.  Analysis of multiple genomic sequence alignments: a web resource, online tools, and lessons learned from analysis of mammalian SCL loci. , 2004, Genome research.

[31]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..

[32]  P. Stadler,et al.  Secondary structure prediction for aligned RNA sequences. , 2002, Journal of molecular biology.

[33]  T. Gregory Dewey,et al.  A Sequence Alignment Algorithm with an Arbitrary Gap Penalty Function , 2001, J. Comput. Biol..

[34]  D. Bartel,et al.  One sequence, two ribozymes: implications for the emergence of new ribozyme folds. , 2000, Science.

[35]  P. Schuster,et al.  RNA folding at elementary step resolution. , 1999, RNA.

[36]  David Sankoff,et al.  The early introduction of dynamic programming into computational biology , 2000, Bioinform..

[37]  G. Deléage,et al.  Secondary structure of P-glycoprotein investigated by circular dichroism and amino acid sequence analysis. , 1998, Biochimica et biophysica acta.

[38]  E. Bornberg-Bauer,et al.  How are model protein structures distributed in sequence space? , 1997, Biophysical journal.

[39]  P. Stadler,et al.  Neutral networks in protein space: a computational study based on knowledge-based potentials of mean force. , 1997, Folding & design.

[40]  J D Palmer,et al.  Intron "sliding" and the diversity of intron positions. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[41]  João Meidanis,et al.  Introduction to computational molecular biology , 1997 .

[42]  R. Lathrop The protein threading problem with sequence amino acid interaction preferences is NP-complete. , 1994, Protein engineering.

[43]  P. Schuster,et al.  From sequences to shapes and back: a case study in RNA secondary structures , 1994, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[44]  M S Waterman,et al.  Sequence alignment and penalty choice. Review of concepts, case studies and implications. , 1994, Journal of molecular biology.

[45]  G. Gonnet,et al.  Exhaustive matching of the entire protein sequence database. , 1992, Science.

[46]  S. Altschul,et al.  A tool for multiple sequence alignment. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[47]  D. Lipman,et al.  The multiple sequence alignment problem in biology , 1988 .

[48]  O. Gotoh Alignment of three biological sequences with an efficient traceback procedure. , 1986, Journal of theoretical biology.

[49]  D. Sankoff Simultaneous Solution of the RNA Folding, Alignment and Protosequence Problems , 1985 .

[50]  C Sander,et al.  On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[51]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[52]  O. Gotoh An improved algorithm for matching biological sequences. , 1982, Journal of molecular biology.

[53]  W. A. Beyer,et al.  Some Biological Sequence Metrics , 1976 .

[54]  D. Sankoff Minimal Mutation Trees of Sequences , 1975 .

[55]  P. Y. Chou,et al.  Prediction of protein conformation. , 1974, Biochemistry.

[56]  S. B. Needleman,et al.  A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.

[57]  Christus,et al.  A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins , 2022 .