H. T. Miller, D. T. Jones, J. M. Thornton
ABSTRACT Protein fold recognition has been approached by threading an amino acid sequence onto a library of folds, calculating a sequence-structure compatibility score, and ranking these scores. Due...
Evolutionary conservation of regulated longevity assurance mechanisms (2007)
McElwee, J.J., Schuster, E., Blanc, E., Piper, M.D., Thomas, J.H., Patel, D.S., ...
Background: To what extent are the determinants of aging in animal species universal? Insulin/insulin-like growth factor (IGF)-1 signaling (IIS) is an evolutionarily conserved (public) regulator of...
Bioinformatics Advance Access published March 24, 2007 (2007)
references marked as “TO BE PUBLISHED ” in the 65,500 references cited by the 43,800 PDB entries. Another problem is that, even where the full reference details are given, there are many cases...
Morphological aspects of oligomeric protein structures (2005)
Ponstingl, H., Kabir, T., Gorse, D., Thornton, J.M.
Features of multimeric proteins are reviewed to shed light on the formation of protein assemblies from a structural perspective. The features comprise biochemical and geometric properties. They are...
Microeconomic principles explain an optimal genome size in bacteria (2005)
Ranea, J.A.G., Grant, A., Thornton, J.M., Orengo, C.A.
Bacteria can clearly enhance their survival by expanding their genetic repertoire. However, the tight packing of the bacterial genome and the fact that the most evolved species do not necessarily...
Ferrer-Costa, C., Shanahan, H. P., Jones, S., Thornton, J. M.
Summary: HTHquery is a web-based service to determine if a protein structure has a helix-turn-helix structural motif which could bind to DNA. It is based on a similarity with a set of structural...
Ferrer-Costa, C., Shanahan, H. P., Jones, S., Thornton, J. M.
Summary: HTH-query is web based service to determine if a protein structure has a Helix-Turn-Helix structural motif which could bind to DNA. It is based on a similarity with a set of structural...
Evolution of protein superfamilies and bacterial genome size (2004)
Ranea, J.A.G., Buchan, D.W.A., Thornton, J.M., Orengo, C.A.
We present the structural annotation of 56 different bacterial species based on the assignment of genes to 816 evolutionary superfamilies in the CATH domain structure database. These assignments have...
An examination of the conservation of surface patch polarity for proteins (2004)
Shanahan, H. P., Thornton, J. M.
Motivation: The solubility of a protein is crucial for its function and is therefore an evolutionary constraint. As the solubility of a protein is related to the distribution of polar and hydrophobic...
An examination of the conservation of surface patch polarity for proteins (2004)
Shanahan, H. P., Thornton, J. M.
Motivation: The solubility of a protein is crucial for its function and is therefore an evolutionary constraint. As the solubility of a protein is related to the distribution of polar and hydrophobic...
An examination of the conservation of surface patch polarity for proteins (2004)
Shanahan, H. P., Thornton, J. M.
Motivation: The solubility of a protein is crucial for its function and is therefore an evolutionary constraint. As the solubility of a protein is related to the distribution of polar and hydrophobic...
Analysis of metabolic networks using a pathway distance metric through linear programming (2003)
Simeonidis, E., Rison, S.C.G., Thornton, J.M., Bogle, I.D.L.
The solution of the shortest path problem in biochemical systems constitutes an important step for studies of their evolution. In this paper, a linear programming (LP) algorithm for calculating...
Wavelet transforms for the characterization and detection of repeating motifs (2002)
Murray, K.B., Gorse, D., Thornton, J.M.
The role of repeating motifs in protein structures is thought to be as modular building blocks which allow an economic way of constructing complex proteins. In this work novel wavelet transform...
Integrating mutation data and structural analysis of the TP53 tumor-suppressor protein (2002)
Martin, A.C.R., Facchiano, A., Cuff, A.L., Hernandez-Boussard, T., Olivier, M., Hainaut, P., ...
TP53 encodes p53, which is a nuclear phosphoprotein with cancer-inhibiting properties. In response to DNA damage, p53 is activated and mediates a set of antiproliferative responses including...
Bray, J.E., Todd, A.E., Pearl, F.M.G., Thornton, J.M., Orengo, C.A.
A consensus approach has been developed for identifying distant structural homologues. This is based on the CATH Dictionary of Homologous Superfamilies (DHS), a database of validated multiple...
Todd, A.E., Orengo, C.A., Thornton, J.M.
A program is described for automatically generating schematic linear representations of protein chains in terms of their structural domains. The program requires the co-ordinates of the chain, the...
Determinants of strand register in antiparallel {beta}-sheets of proteins (1998)
HUTCHINSON, E. G., SESSIONS, R. B., THORNTON, J. M., WOOLFSON, D. N.
Structures of N-termini of helices in proteins (1997)
DOIG, A. J., MACARTHUR, M. W., STAPLEY, B. J., THORNTON, J. M.
Protein clefts in molecular recognition and function (1996)
LASKOWSKI, R. A., LUSCOMBE, N. M., SWINDELLS, M. B., THORNTON, J. M.
ORENGO, C. A., SWINDELLS, M. B., MICHIE, A. D., ZVELEBIL, M. J., DRISCOLL, P. C., WATERFIELD, M. D., ...
An algorithm for automatically generating protein topology cartoons (1994)
Flores, T.P., Moss, D.S., Thornton, J.M.
An algorithm is described for automatically generating protein topology cartoons. This algorithm optimally places circles and triangles depicting ß-heikes and ß-strands respectively giving a...
The BC loop in poliovirus coat protein VP1: an ideal acceptor site for major insertions (1994)
In poliovirus the BC loop of the VP1 coat protein is hypervariable and can accommodate numerous foreign sequences introduced by genetic engineering. This paper examines the characteristics of the VP1...
Identification and classification of protein fold families (1993)
Orengo, C.A, Flores, T.P., Taylor, W.R., Thornton, J.M.
We have developed a method for identifying fold families in the protein structure data bank. Pairwise sequence alignments are first performed to extract families of homologous proteins having...
{beta}-Turns and their distortions: a proposed new nomenclature (1990)
Using the new version of a Protein Structural Database, BIPED, β-tums have been extracted from 58 non-identical proteins (resolution ≤ 2 Å) using the standard criteria that the distance between...
Principles of protein-protein interactions.
This review examines protein complexes in the Brookhaven Protein Databank to gain a better understanding of the principles governing the interactions involved in protein-protein recognition. The...
NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions.
Luscombe, N M, Laskowski, R A, Thornton, J M
Proteins that bind to DNA are found in all areas of genetic activity within the cell. To help understand how these proteins perform their various functions, it is useful to analyse which residues are...
The CATH Database provides insights into protein structure/function relationships.
Orengo, C A, Pearl, F M, Bray, J E, Todd, A E, Martin, A C, Lo Conte, L, ...
We report the latest release (version 1.4) of the CATH protein domains database (http://www.biochem.ucl.ac.uk/bsm/cath). This is a hierarchical classification of 13 359 protein domain structures into...
A study into the effects of protein binding on nucleotide conformation.
In this study, we examine the effects of binding to protein upon nucleotide conformation, by the comparison of X-ray crystal structures of free and protein-bound nucleotides. A dataset of...
Semi-empirical conformational energy calculations were performed for the mononucleotides 5'-AMP, NMN+ and 3'-AMP. Only intramolecular forces are considered. Essentially all conformational states were...
Location of 'continuous' antigenic determinants in the protruding regions of proteins.
Thornton, J M, Edwards, M S, Taylor, W R, Barlow, D J
A simple method is described to locate 'antigenic' peptides from the alpha-carbon co-ordinates of a protein, based on protrusion from the protein's globular surface. A good correlation is found...
Harding, S E, Horton, J C, Jones, S, Thornton, J M, Winzor, D J
An interactive program is described for calculating the second virial coefficient contribution to the thermodynamic nonideality of solutions of rigid macromolecules based on their triaxial...
Principles of protein-protein interactions.
This review examines protein complexes in the Brookhaven Protein Databank to gain a better understanding of the principles governing the interactions involved in protein-protein recognition. The...
NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions.
Luscombe, N M, Laskowski, R A, Thornton, J M
Proteins that bind to DNA are found in all areas of genetic activity within the cell. To help understand how these proteins perform their various functions, it is useful to analyse which residues are...
The CATH Database provides insights into protein structure/function relationships.
Orengo, C A, Pearl, F M, Bray, J E, Todd, A E, Martin, A C, Lo Conte, L, ...
We report the latest release (version 1.4) of the CATH protein domains database (http://www.biochem.ucl.ac.uk/bsm/cath). This is a hierarchical classification of 13 359 protein domain structures into...
A study into the effects of protein binding on nucleotide conformation.
In this study, we examine the effects of binding to protein upon nucleotide conformation, by the comparison of X-ray crystal structures of free and protein-bound nucleotides. A dataset of...
Semi-empirical conformational energy calculations were performed for the mononucleotides 5'-AMP, NMN+ and 3'-AMP. Only intramolecular forces are considered. Essentially all conformational states were...
Location of 'continuous' antigenic determinants in the protruding regions of proteins.
Thornton, J M, Edwards, M S, Taylor, W R, Barlow, D J
A simple method is described to locate 'antigenic' peptides from the alpha-carbon co-ordinates of a protein, based on protrusion from the protein's globular surface. A good correlation is found...
Harding, S E, Horton, J C, Jones, S, Thornton, J M, Winzor, D J
An interactive program is described for calculating the second virial coefficient contribution to the thermodynamic nonideality of solutions of rigid macromolecules based on their triaxial...
Identification, classification, and analysis of beta-bulges in proteins.
Chan, A. W., Hutchinson, E. G., Harris, D., Thornton, J. M.
A beta-bulge is a region of irregularity in a beta-sheet involving two beta-strands. It usually involves two or more residues in the bulged strand opposite to a single residue on the adjacent strand....
Comparison of conformational characteristics in structurally similar protein pairs.
Flores, T. P., Orengo, C. A., Moss, D. S., Thornton, J. M.
Although it is known that three-dimensional structure is well conserved during the evolutionary development of proteins, there have been few studies that consider other parameters apart from...
Modeling studies of the change in conformation required for cleavage of limited proteolytic sites.
Hubbard, S. J., Eisenmenger, F., Thornton, J. M.
Previous analyses of limited proteolytic sites within native, folded protein structures have shown that a significant conformational change is required in order to facilitate binding into the active...
A revised set of potentials for beta-turn formation in proteins.
Hutchinson, E. G., Thornton, J. M.
Three thousand eight hundred ninety-nine beta-turns have been identified and classified using a nonhomologous data set of 205 protein chains. These were used to derive beta-turn positional potentials...
Buried waters and internal cavities in monomeric proteins.
Williams, M. A., Goodfellow, J. M., Thornton, J. M.
We have analyzed the buried water molecules and internal cavities in a set of 75 high-resolution, nonhomologous, monomeric protein structures. The number of hydrogen bonds formed between each water...
Orengo, C. A., Swindells, M. B., Michie, A. D., Zvelebil, M. J., Driscoll, P. C., Waterfield, M. D., ...
An unexpected structural similarity is described between the pleckstrin homology (PH) domain and verotoxin. This similarity has escaped detection primarily due to the differences in topology that...
Protein clefts in molecular recognition and function.
Laskowski, R. A., Luscombe, N. M., Swindells, M. B., Thornton, J. M.
One of the primary factors determining how proteins interact with other molecules is the size of clefts in the protein's surface. In enzymes, for example, the active site is often characterized by a...
PROMOTIF--a program to identify and analyze structural motifs in proteins.
Hutchinson, E. G., Thornton, J. M.
We describe a suite of programs, PROMOTIF, that analyzes a protein coordinate file and provides details about the structural motifs in the protein. The program currently analyzes the following...
Wallace, A. C., Laskowski, R. A., Thornton, J. M.
It is well established that sequence templates (e.g., PROSITE) and databases are powerful tools for identifying biological function and tertiary structure for an unknown protein sequence. Here we...
Structures of N-termini of helices in proteins.
Doig, A. J., MacArthur, M. W., Stapley, B. J., Thornton, J. M.
We have surveyed 393 N-termini of alpha-helices and 156 N-termini of 3(10)-helices in 85 high resolution, non-homologous protein crystal structures for N-cap side-chain rotamer preferences, hydrogen...
Wallace, A. C., Borkakoti, N., Thornton, J. M.
It is well established that sequence templates such as those in the PROSITE and PRINTS databases are powerful tools for predicting the biological function and tertiary structure for newly derived...
Determinants of strand register in antiparallel beta-sheets of proteins.
Hutchinson, E. G., Sessions, R. B., Thornton, J. M., Woolfson, D. N.
Antiparallel beta-sheets present two distinct environments to inter-strand residue pairs: beta(A,HB) sites have two backbone hydrogen bonds; whereas at beta(A,NHB) positions backbone hydrogen bonding...
Domain assignment for protein structures using a consensus approach: characterization and analysis.
Jones, S., Stewart, M., Michie, A., Swindells, M. B., Orengo, C., Thornton, J. M.
A consensus approach for the assignment of structural domains in proteins is presented. The approach combines a number of previously published algorithms, and takes advantage of the elevated accuracy...
Nagano, N., Hutchinson, E. G., Thornton, J. M.
Automated methods for identifying and characterizing regular beta-barrels from coordinate data have been developed to analyze and classify various kinds of barrel structures based on geometric...
Protein structural topology: Automated analysis and diagrammatic representation.
Westhead, D. R., Slidel, T. W., Flores, T. P., Thornton, J. M.
The topology of a protein structure is a highly simplified description of its fold including only the sequence of secondary structure elements, and their relative spatial positions and approximate...
Factors limiting the performance of prediction-based fold recognition methods.
In the past few years, a new generation of fold recognition methods has been developed, in which the classical sequence information is combined with information obtained from secondary structure and,...
Prediction of the location and type of beta-turns in proteins using neural networks.
Shepherd, A. J., Gorse, D., Thornton, J. M.
A neural network has been used to predict both the location and the type of beta-turns in a set of 300 nonhomologous protein domains. A substantial improvement in prediction accuracy compared with...