PubRank

J M Thornton

Author PubWeight™ 506.18‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 1992 44.38
2 CATH--a hierarchic classification of protein domain structures. Structure 1997 29.95
3 AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 1996 29.55
4 LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng 1995 19.22
5 Satisfying hydrogen bonding potential in proteins. J Mol Biol 1994 14.79
6 Principles of protein-protein interactions. Proc Natl Acad Sci U S A 1996 14.51
7 A mutation data matrix for transmembrane proteins. FEBS Lett 1994 13.49
8 PDBsum: a Web-based database of summaries and analyses of all PDB structures. Trends Biochem Sci 1997 12.04
9 Main-chain bond lengths and bond angles in protein structures. J Mol Biol 1993 9.80
10 PQS: a protein quaternary structure file server. Trends Biochem Sci 1998 9.24
11 Stereochemical quality of protein structure coordinates. Proteins 1992 9.18
12 Protein structural topology: Automated analysis and diagrammatic representation. Protein Sci 1999 8.24
13 A new approach to protein fold recognition. Nature 1992 8.17
14 Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res 2001 7.27
15 PROMOTIF--a program to identify and analyze structural motifs in proteins. Protein Sci 1996 6.76
16 A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry 1994 6.64
17 Evolution of function in protein superfamilies, from a structural perspective. J Mol Biol 2001 6.63
18 Comparison of functional annotation schemes for genomes. Funct Integr Genomics 2000 5.17
19 Protein superfamilies and domain superfolds. Nature 1994 5.11
20 A revised set of potentials for beta-turn formation in proteins. Protein Sci 1994 4.97
21 Analysis and prediction of the different types of beta-turn in proteins. J Mol Biol 1988 4.88
22 Influence of proline residues on protein conformation. J Mol Biol 1991 4.87
23 Helix geometry in proteins. J Mol Biol 1988 4.66
24 Analysis of protein-protein interaction sites using surface patches. J Mol Biol 1997 4.51
25 Assigning genomic sequences to CATH. Nucleic Acids Res 2000 4.22
26 Protein clefts in molecular recognition and function. Protein Sci 1996 4.20
27 Disulphide bridges in globular proteins. J Mol Biol 1981 4.06
28 Protein-protein interactions: a review of protein dimer structures. Prog Biophys Mol Biol 1995 3.98
29 An overview of the structures of protein-DNA complexes. Genome Biol 2000 3.90
30 Identification and classification of protein fold families. Protein Eng 1993 3.58
31 TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. Protein Sci 1997 3.50
32 Protein-DNA interactions: A structural analysis. J Mol Biol 1999 3.38
33 Ion-pairs in proteins. J Mol Biol 1983 3.37
34 Continuous and discontinuous protein antigenic determinants. Nature 1986 3.26
35 Molecular recognition. Conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors. J Mol Biol 1991 3.04
36 Protein-protein interfaces: analysis of amino acid conservation in homodimers. Proteins 2001 3.00
37 Knowledge-based prediction of protein structures and the design of novel molecules. Nature 1987 2.99
38 Discriminating between homodimeric and monomeric proteins in the crystalline state. Proteins 2000 2.96
39 Beta-hairpin families in globular proteins. Nature 1985 2.95
40 Protein-RNA interactions: a structural analysis. Nucleic Acids Res 2001 2.92
41 Prediction of protein-protein interaction sites using patch analysis. J Mol Biol 1997 2.91
42 Conformation of beta-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering. J Mol Biol 1989 2.86
43 The CATH domain structure database. Methods Biochem Anal 2003 2.83
44 NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions. Nucleic Acids Res 1997 2.81
45 Beta-turns and their distortions: a proposed new nomenclature. Protein Eng 1990 2.67
46 The CATH Database provides insights into protein structure/function relationships. Nucleic Acids Res 1999 2.57
47 Analysis of main chain torsion angles in proteins: prediction of NMR coupling constants for native and random coil conformations. J Mol Biol 1996 2.50
48 Domain assignment for protein structures using a consensus approach: characterization and analysis. Protein Sci 1998 2.41
49 Identification, classification, and analysis of beta-bulges in proteins. Protein Sci 1993 2.36
50 Intrinsic phi, psi propensities of amino acids, derived from the coil regions of known structures. Nat Struct Biol 1995 2.32
51 Buried waters and internal cavities in monomeric proteins. Protein Sci 1994 2.30
52 Three-dimensional structure analysis of PROSITE patterns. J Mol Biol 1999 2.25
53 Location of 'continuous' antigenic determinants in the protruding regions of proteins. EMBO J 1986 2.22
54 Antibody-antigen interactions: contact analysis and binding site topography. J Mol Biol 1996 2.22
55 Recognition of super-secondary structure in proteins. J Mol Biol 1984 2.21
56 The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli. J Mol Biol 2001 2.15
57 Sequences annotated by structure: a tool to facilitate the use of structural information in sequence analysis. Protein Eng 1998 2.12
58 HERA--a program to draw schematic diagrams of protein secondary structures. Proteins 1990 2.00
59 Conservation helps to identify biologically relevant crystal contacts. J Mol Biol 2001 1.98
60 Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases. Protein Sci 1996 1.97
61 Distributions of water around amino acid residues in proteins. J Mol Biol 1988 1.90
62 Modelling protein unfolding: hen egg-white lysozyme. Protein Eng 1997 1.88
63 Prediction of super-secondary structure in proteins. Nature 1983 1.84
64 Comparison of conformational characteristics in structurally similar protein pairs. Protein Sci 1993 1.84
65 Amino and carboxy-terminal regions in globular proteins. J Mol Biol 1983 1.82
66 Pi-pi interactions: the geometry and energetics of phenylalanine-phenylalanine interactions in proteins. J Mol Biol 1991 1.81
67 SIRIUS. An automated method for the analysis of the preferred packing arrangements between protein groups. J Mol Biol 1990 1.80
68 Amino/aromatic interactions in proteins: is the evidence stacked against hydrogen bonding? J Mol Biol 1994 1.77
69 Structural families in loops of homologous proteins: automatic classification, modelling and application to antibodies. J Mol Biol 1996 1.71
70 Validation of protein models derived from experiment. Curr Opin Struct Biol 1998 1.70
71 Protein folds and functions. Structure 1998 1.69
72 The CATH Dictionary of Homologous Superfamilies (DHS): a consensus approach for identifying distant structural homologues. Protein Eng 2000 1.67
73 On the conformation of proteins: the handedness of the connection between parallel beta-strands. J Mol Biol 1977 1.66
74 Modeling studies of the change in conformation required for cleavage of limited proteolytic sites. Protein Sci 1994 1.63
75 A rapid classification protocol for the CATH Domain Database to support structural genomics. Nucleic Acids Res 2001 1.61
76 Evolution of protein function, from a structural perspective. Curr Opin Chem Biol 1999 1.61
77 A topological model for hepatitis B surface antigen. Intervirology 1992 1.59
78 From protein structure to function. Curr Opin Struct Biol 1999 1.58
79 Alpha plus beta folds revisited: some favoured motifs. Structure 1993 1.57
80 Determinants of strand register in antiparallel beta-sheets of proteins. Protein Sci 1998 1.55
81 Protein recognition of adenylate: an example of a fuzzy recognition template. J Mol Biol 1996 1.54
82 Structures of N-termini of helices in proteins. Protein Sci 1997 1.53
83 Recurrence of a binding motif? Nature 1993 1.50
84 Protein domain interfaces: characterization and comparison with oligomeric protein interfaces. Protein Eng 2000 1.43
85 The distribution of charged groups in proteins. Biopolymers 1986 1.39
86 Potential energy functions for threading. Curr Opin Struct Biol 1996 1.39
87 Analysis and prediction of carbohydrate binding sites. Protein Eng 2000 1.39
88 An algorithm for automatically generating protein topology cartoons. Protein Eng 1994 1.38
89 Deviations from planarity of the peptide bond in peptides and proteins. J Mol Biol 1996 1.36
90 On the conformation of proteins: the handedness of the beta-strand-alpha-helix-beta-strand unit. J Mol Biol 1976 1.34
91 Prediction of the location and type of beta-turns in proteins using neural networks. Protein Sci 1999 1.30
92 An atlas of protein topology cartoons available on the World-Wide Web. Trends Biochem Sci 1998 1.28
93 On the molecular discrimination between adenine and guanine by proteins. Nucleic Acids Res 2001 1.26
94 Atomic environments of arginine side chains in proteins. Protein Eng 1993 1.23
95 Using the CATH domain database to assign structures and functions to the genome sequences. Biochem Soc Trans 2000 1.22
96 Rebuilding flavodoxin from C alpha coordinates: a test study. Proteins 1989 1.22
97 Assessment of conformational parameters as predictors of limited proteolytic sites in native protein structures. Protein Eng 1998 1.22
98 On the conformation of proteins: an analysis of beta-pleated sheets. J Mol Biol 1977 1.21
99 Assessment of comparative modeling in CASP2. Proteins 1997 1.21
100 COVOL: an interactive program for evaluating second virial coefficients from the triaxial shape or dimensions of rigid macromolecules. Biophys J 1999 1.21
101 Correlation of observed fold frequency with the occurrence of local structural motifs. J Mol Biol 1999 1.19
102 The Greek key motif: extraction, classification and analysis. Protein Eng 1993 1.19
103 Analysis of domain structural class using an automated class assignment protocol. J Mol Biol 1996 1.18
104 Towards an understanding of the arginine-aspartate interaction. J Mol Biol 1992 1.18
105 Conformation of beta hairpins in protein structures: classification and diversity in homologous structures. Methods Enzymol 1991 1.18
106 Depicting topology and handedness in jellyroll structures. FEBS Lett 1992 1.16
107 Substrate recognition by proteinases. Faraday Discuss 1992 1.14
108 An analysis of the structure of triose phosphate isomerase and its comparison with lactate dehydrogenase. J Mol Biol 1978 1.14
109 Non-randomness in side-chain packing: the distribution of interplanar angles. Proteins 1997 1.12
110 SPINE bioinformatics and data-management aspects of high-throughput structural biology. Acta Crystallogr D Biol Crystallogr 2006 1.08
111 Small-molecule metabolism: an enzyme mosaic. Trends Biotechnol 2001 1.08
112 X-SITE: use of empirically derived atomic packing preferences to identify favourable interaction regions in the binding sites of proteins. J Mol Biol 1996 1.08
113 Structural and sequence patterns in the loops of beta alpha beta units. Protein Eng 1987 1.05
114 Recurring structural motifs in proteins with different functions. Curr Biol 1993 1.02
115 Analysis of protein main-chain solvation as a function of secondary structure. J Mol Biol 1991 1.01
116 Analysis, design and modification of loop regions in proteins. Bioessays 1988 0.99
117 HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif. Bioinformatics 2005 0.99
118 Just noticeable and objectionable group delays in digital hearing aids. J Am Acad Audiol 2000 0.98
119 Protein side-chain conformation: a systematic variation of chi 1 mean values with resolution - a consequence of multiple rotameric states? Acta Crystallogr D Biol Crystallogr 1999 0.98
120 Characterization of atypical Aeromonas salmonicida by different methods. Syst Appl Microbiol 1998 0.98
121 Protein motifs and data-base searching. Trends Biochem Sci 1989 0.96
122 A study into the effects of protein binding on nucleotide conformation. Nucleic Acids Res 1993 0.96
123 Small binding proteins selected from a combinatorial repertoire of knottins displayed on phage. J Mol Biol 1998 0.95
124 Dihydrofolate reductase: a potential drug target in trypanosomes and leishmania. J Comput Aided Mol Des 1998 0.95
125 On the conformation of proteins: hydrophobic ordering of strands in beta-pleated sheets. J Mol Biol 1977 0.95
126 1H NMR structure of an antifungal gamma-thionin protein SIalpha1: similarity to scorpion toxins. Proteins 1998 0.93
127 Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing. Proteins 1995 0.93
128 Influence of secondary structure on the hydration of serine, threonine and tyrosine residues in proteins. Protein Eng 1990 0.93
129 Prediction of protein structure from amino acid sequence. Nature 1978 0.93
130 Contemporary approaches to protein structure classification. Bioessays 1998 0.93
131 Conformational analysis of protein structures derived from NMR data. Proteins 1993 0.92
132 The (betaalpha)(8) glycosidases: sequence and structure analyses suggest distant evolutionary relationships. Protein Eng 2001 0.92
133 New tools and resources for analysing protein structures and their interactions. Acta Crystallogr D Biol Crystallogr 1998 0.91
134 Quantitative determination of the conformation of ATP in aqueous solution using the lanthanide cations as nuclear-magnetic-resonance probes. Eur J Biochem 1975 0.91
135 The application of hydrogen bonding analysis in X-ray crystallography to help orientate asparagine, glutamine and histidine side chains. Protein Eng 1995 0.90
136 Comparison of the calcium- and magnesium-induced structural changes of troponin--C. A proton magnetic resonance study. Biochim Biophys Acta 1978 0.90
137 Accommodating sequence changes in beta-hairpins in proteins. J Mol Biol 1993 0.90
138 Classifying a protein in the CATH database of domain structures. Acta Crystallogr D Biol Crystallogr 1998 0.89
139 Protein fold recognition by sequence threading: tools and assessment techniques. FASEB J 1996 0.88
140 Topological and stereochemical restrictions in beta-sandwich protein structures. Protein Eng 1993 0.88
141 Protein structure. Prediction of progress at last. Nature 1991 0.88
142 Design, synthesis and structure of a zinc finger with an artificial beta-turn. J Mol Biol 1998 0.88
143 An analysis of the three-dimensional structure of chicken triose phosphate isomerase. Biochem Soc Trans 1977 0.88
144 HydroCoils, occlusion rates, and outcomes: a large single-center study. AJNR Am J Neuroradiol 2010 0.88
145 Calcium binding by troponin-C. A proton magnetic resonance study. J Mol Biol 1977 0.87
146 Protein structure prediction. Curr Opin Biotechnol 1998 0.87
147 The BC loop in poliovirus coat protein VP1: an ideal acceptor site for major insertions. Protein Eng 1994 0.87
148 The geometries of interacting arginine-carboxyls in proteins. FEBS Lett 1987 0.87
149 Barrel structures in proteins: automatic identification and classification including a sequence analysis of TIM barrels. Protein Sci 1999 0.86
150 Functional and modelling studies of the binding of human monoclonal anti-DNA antibodies to DNA. Mol Immunol 1996 0.86
151 Towards meeting the Paracelsus Challenge: The design, synthesis, and characterization of paracelsin-43, an alpha-helical protein with over 50% sequence identity to an all-beta protein. Proteins 1996 0.85
152 Conformational energy calculations for dinucleotide molecules. A systematic study of dinucleotide conformation, with application to diadenosine pyrophosphate. Biopolymers 1976 0.85
153 DOMPLOT: a program to generate schematic diagrams of the structural domain organization within proteins, annotated by ligand contacts. Protein Eng 1999 0.84
154 Protein structure. The shape of things to come? Nature 1988 0.83
155 Ventricular activation during sympathetic imbalance and its computational reconstruction. J Appl Physiol (1985) 2001 0.82
156 Multiple solution conformations of the integrin-binding cyclic pentapeptide cyclo(-Ser-D-Leu-Asp-Val-Pro-). Analysis of the (phi, psi) space available to cyclic pentapeptides. Eur J Biochem 1996 0.82
157 Enhanced DNA binding capacity on up-regulated epidermal wild-type p53 in vitiligo by H2O2-mediated oxidation: a possible repair mechanism for DNA damage. FASEB J 2009 0.81
158 Structural similarity between the pleckstrin homology domain and verotoxin: the problem of measuring and evaluating structural similarity. Protein Sci 1995 0.81
159 Amino acid architecture and the distribution of polar atoms on the surfaces of proteins. Biopolymers 2005 0.80
160 Electrostatic interactions in proteins. Nature 1982 0.80
161 Haplotypes in the CTLA4 region are associated with coeliac disease in the Irish population. Genes Immun 2006 0.80
162 On the conformation of proteins: towards the prediction of strand arrangements in beta-pleated sheets. J Mol Biol 1977 0.80
163 Molecular modelling and epitope prediction of gp29 from lymphatic filariae. Mol Biochem Parasitol 1993 0.79
164 An examination of the conservation of surface patch polarity for proteins. Bioinformatics 2004 0.79
165 Macromolecular structure information and databases. The EU BRIDGE Database Project Consortium. Trends Biochem Sci 1996 0.78
166 Chromosome 5q candidate genes in coeliac disease: genetic variation at IL4, IL5, IL9, IL13, IL17B and NR3C1. Tissue Antigens 2005 0.78
167 NMR and crystallography--complementary approaches to structure determination. Trends Biotechnol 1994 0.78
168 A study of structural determinants in the interleukin-1 fold. Protein Eng 1993 0.78
169 Factors limiting the performance of prediction-based fold recognition methods. Protein Sci 1999 0.78
170 Long loops in proteins. Protein Eng 1995 0.78
171 Conformational energy calculations for dinucleotide molecules: a study of the nucleotide coenzyme nicotinamide adenine dinucleotide (NAD+). Biopolymers 1977 0.77
172 Solution structure of a biologically active cyclic LDV peptide analogue containing a type II' beta-turn mimetic. Int J Pept Protein Res 1996 0.77
173 A novel method for the modelling of peptide ligands to their receptors. Protein Eng 1991 0.77
174 Conformation of terminal regions in proteins. Nature 1982 0.76
175 Molecular recognition by proteins: protein-ligand interactions from a structural perspective. Biochem Soc Trans 1996 0.76
176 Structural studies of Impatiens balsamina antimicrobial protein (Ib-AMP1). Biochemistry 1998 0.76
177 An extension of secondary structure prediction towards the prediction of tertiary structure. FEBS Lett 1991 0.76
178 Antibody modelling. Tackling a loopy problem. Nature 1990 0.75
179 Polymerase chain reaction (PCR)-based typing analysis of atypical isolates of the fish pathogen Aeromonas salmonicida. Syst Appl Microbiol 1999 0.75
180 Conformational energy calculations for dinucleotide molecules. A study of the component mononucleotide adenosine 3'-monophosphate. Biochem J 1975 0.75
181 Haplotype variation at the IBD5/SLC22A4 locus (5q31) in coeliac disease in the Irish population. Tissue Antigens 2004 0.75
182 Peptide-protein interactions: an overview. Q Rev Biophys 1993 0.75
183 Developing a rural nursing clinic. Nurse Educ 1983 0.75
184 Prediction of protein structure from amino acid sequence. Biochem Soc Trans 1978 0.75
185 Structure prediction and modelling. Curr Opin Biotechnol 1991 0.75
186 Proton magnetic resonance study of troponin-C. FEBS Lett 1976 0.75
187 Amino acid sequence templates derived from recurrent turn motifs in proteins: critical evaluation of their predictive power. Protein Eng 1989 0.75