Prediction of protein function from structure: insights from methods for the detection of local structural similarities.

[1]  Janet M. Thornton,et al.  From protein structure to biochemical function? , 2004, Journal of Structural and Functional Genomics.

[2]  Gerard J Kleywegt,et al.  Evaluation of protein fold comparison servers , 2003, Proteins.

[3]  Janet M. Thornton,et al.  The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data , 2004, Nucleic Acids Res..

[4]  I. Rigoutsos,et al.  Geometric Hashing , 1997, IEEE Computational Science and Engineering.

[5]  L. Pearl.  Similarity of active-site structures , 1993, Nature.

[6]  S Karlin,et al.  Characterizations of diverse residue clusters in protein three-dimensional structures. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[7]  H. Wolfson,et al.  Recognition of Functional Sites in Protein Structures☆ , 2004, Journal of Molecular Biology.

[8]  F. Ferrè,et al.  Protein surface similarities: a survey of methods to describe and compare protein surfaces , 2000, Cellular and Molecular Life Sciences CMLS.

[9]  K Henrick,et al.  Electronic Reprint Biological Crystallography Secondary-structure Matching (ssm), a New Tool for Fast Protein Structure Alignment in Three Dimensions Biological Crystallography Secondary-structure Matching (ssm), a New Tool for Fast Protein Structure Alignment in Three Dimensions , 2022 .

[10]  C. Sander,et al.  Dali: a network tool for protein structure comparison. , 1995, Trends in biochemical sciences.

[11]  Nicholas Ayache,et al.  A geometric algorithm to find small but highly similar 3D substructures in proteins , 1998, Bioinform..

[12]  Gail J. Bartlett,et al.  Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families. , 2005, Journal of molecular biology.

[13]  Robert B. Russell,et al.  Annotation in three dimensions , 2003 .

[14]  Robert B. Russell,et al.  Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures , 2003, Nucleic Acids Res..

[15]  R. Russell,et al.  Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution. , 1998, Journal of molecular biology.

[16]  Frances M. G. Pearl,et al.  The CATH domain structure database. , 2005, Methods of biochemical analysis.

[17]  C. Orengo,et al.  Plasticity of enzyme active sites. , 2002, Trends in biochemical sciences.

[18]  William R. Taylor,et al.  Structure Motif Discovery and Mining the PDB , 2002, German Conference on Bioinformatics.

[19]  S. J. Campbell,et al.  Ligand binding: functional site location, similarity and docking. , 2003, Current opinion in structural biology.

[20]  Jie Liang,et al.  Inferring functional relationships of proteins from local sequence and spatial surface patterns. , 2003, Journal of molecular biology.

[21]  Tim J. P. Hubbard,et al.  SCOP database in 2004: refinements integrate structure and sequence family data , 2004, Nucleic Acids Res..

[22]  I. Jonassen,et al.  Discovery of local packing motifs in protein structures , 1999, Proteins.

[23]  D. Leckband,et al.  Intermolecular forces in biology , 2001, Quarterly Reviews of Biophysics.

[24]  Janet M. Thornton,et al.  An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis , 2003, Bioinform..

[25]  Donald L. Kreher,et al.  Combinatorial algorithms: generation, enumeration, and search , 1998, SIGA.

[26]  Frances M. G. Pearl,et al.  Recognizing the fold of a protein structure , 2003, Bioinform..

[27]  Gerard J Kleywegt,et al.  Déjà vu all over again: finding and analyzing protein structure similarities. , 2004, Structure.

[28]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..