PROTEIN BIOINFORMATICS

An Algorithmic Approach to Sequence and Structure Analysis

Ingvar Eidhammer, Inge Jonassen, William R. Taylor

Additional bibliography - June 7., 2005

• Chapter 2 - Pairwise Local Alignment and Database Search
  • Itoh M, Goto S., Akutsu T., Kanehisa M., 2005. Fast and accurate database homology search using upper bounds of local alignment scores. Bioinforamtics 21 (7) 912-921
  • Maricel G.K. et al., 2005. A structure based method for protein sequence alignment. Bioinforamtics 21 (8) 1451-1456
• Chapter 3 - Statistical Analysis
  • Chen Z 2003 Assessing sequence comparison methods with the average precision criterion Bioinformatics 19 (18) 2456-2460
  • Nozaki Y. and Bellgard M., 2005. Statistical evaluation and comparison of a pairwise alignemnt algorithm that a priori assigns the number of gaps rather than employing gap penalties. Bioinformatics 21 (8) 1421-1428.
• Chapter 4 - Multiple Global Alignment and Phylogenetic Trees
  • Multiple alignment
    • O'Sullivan, O et al. 2004 3DCoffee: Combining Protein Sequences and Structures within Multiple Sequence Alignments. J. Mol. Biol. 340, 385-395
    • Wang Y, Li K-B 2004 An adaptive and iterative algorithm for refining multiple sequence alignment Comp. Biol. Chem. 28, 141-148
    • C.L. Lu and Y.P. Huang 2005 A memory-efficient algorithm for multiple sequence alignment with constraints. Bioinformatics 21 (1), 20-30.
    • Wallace I.M. and O'Sullivan O. and Higgins D.G. 2005 Evaluation of iterative alignment algorithms for multiple alignment. Bioinformatics 21 (8), 1408-1414.
  • Phylogeny
    • Otu HH, Sayood K 2003 A new sequence distance measure for phylogenetic tree construction Bioinformatics 19 (16) 2122-2130
• Chapter 5 - Scoring Matrices
  • Yu Y-K., Altschul S.F.,2005 The construction of amino acid substitutions matrices for the comparison of proteins with non-standard compositions. Bioinformatics 21 (7) 902-911
• Chapter 6 - Profiles
  • Profile
    • Edgar RC, Sjølander K 2004 A comparison of scoring functions for protein sequence profile alignment Bioinformatics 20 (8) 1301
  • HMM profiles
    • Edgar RC, Sjølander K 2004 COACH: profile-profile alignment of protein families using hidden Markov models 20 (8) 1309
  • Weight Matrix
    • Zheng W-M. 2005. Relation between weight matrix and substitutions matrix: motif search by similarity. Bioinformatics 21 (7) 938-943
• Chapter 10 - Geometric Techniques
  • Shih ESC, Hwang M-J 2003 Protein structure comparison by probability-based matching of secondary structure elements. Bioinformatics 19 (6) 735-741
• Other Structure Comparison Methods
  • L. Chen and T. Zhou and Y. Tang (2005) Protein structure alignment by deterministic annealing. Bioinformatics 21 (1) 51-62
• Chapter 12 - Significance and Assessment of Structure Comparisons
  • Krasnogor H, Pelta DA 2004 Measuring the similarity of protein structures by means of the universal similarity metric Bioinformatics 20 (7) 1015-1021
  • R. Kolodny and P. Koehl and M. Levitt (2005). Comprehensive Evaluation of Protein Structure Alignment Methods: Scoring by Geometric Measures. JMB 346, 1173-1188.
• Chapter 13 - Multiple Structure Comparison
  • Schmollinger M et al. (2004) ParSeq: searching motifs with structural and biochemical properties Bioinformatics 20 (9) 1459-1461
  • Ye Y. and Godzik A. (2005) Multiple flexible structure alignment using partial order graphs. Bioinformatics 21 (10) 2362-2369.
• Chapter 14 - Protein Structure Classification
  • Kihara D, Skolnick J. 2003 The PDB is a Covering Set of Small Protein Structures J. Mol. Biol. 334 793-802
  • Tendulkar AV et al. 2003 Parameterization and Classification of the Protein Universe via Geometric Techniques J. Mol. Biol. 2003 157-172
  • Via A., Zanzoni A., Helmer-Citterich M. 2005. Seq2Struct: a resource for establishing sequence-structure links. Bioinformatics 21 (4) 551-553.
  • Torrance G.M. et al. 2005. Protein structure topological comparison, discovery and matching service. Bioinformatics 21 (10) 2537-2538.