EVALUATING LOCAL STRUCTURE ALPHABETS FOR PROTEIN STRUCTURE PREDICTION

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EVALUATING LOCAL STRUCTURE ALPHABETS FOR PROTEIN STRUCTURE PREDICTION (2003)

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by Rachel Karchin

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7 - 1 self

Citations

8546	Gapped BLAST and PSI-BLAST: a new generation of protein database search programs - Altschul, Madden, et al. - 1997
8132	Basic local alignment search tool - Altschul, Carrol, et al. - 1990
6582	Neural Networks for Pattern Recognition - Bishop
2092	Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features, Biopolymers 22 - Kabsch, Sander - 1983
1979	R: R: A language for data analysis and graphics - Ihaka, Gentleman - 1996
1385	The Protein Data Bank - Berman, Westbrook, et al.
1338	Profile hidden Markov models - Eddy - 1998
1211	Biological Sequence Analysis: Probabilistic models of Proteins and Nucleic Acids. Cambridge U - Durbin, Eddy, et al. - 1999
943	Protein secondary structure prediction based on position-specific scoring matrices - Jones - 1999
856	Protein structure comparison by alignment of distance matrices - Holm, Sander - 1993
652	The Protein Data Bank: A computer-based archival file for macromolecular structures - Bernstein, Koetzle, et al. - 1977
540	Supervised and Unsupervised Discretization of Continuous Features. InMachine learning - Dougherty, Kohavi, et al. - 1995
534	Principles that govern the folding of protein chains, Science 181 - Anfinsen - 1973
516	Introduction to Protein Structure - Branden, Tooze - 1991
406	A Solution for the Best Rotation to Relate Two Sets of Vectors - KABSCH - 1976
387	Statistical analysis of circular data - Fisher - 1995
384	Mapping the protein universe - Holm, Sander - 1996
338	Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. - Garnier, Osguthorpe, et al. - 1978
329	A method to identify protein sequences that fold into a known three-dimensional structure - Bowie, Luthy, et al. - 1991
324	Knowledge-based protein secondary structure assignment - Frishman, Argos - 1995
322	The relation between the divergence of sequence and structure in proteins - Chothia, Lesk - 1986
316	Assessing the accuracy of prediction algorithms for classification: an overview - Baldi, Brunak, et al. - 2000
277	Probabilistic Interpretation of Feedforward Classification Network Outputs, with Relationships to Statistical Pattern Recognition,‖ Neurocomputing—Algorithms, Architectures and Applications, - Bridle - 1989
263	Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching - Gribskov, Robinson - 1996
242	A Discriminative Framework for Detecting Remote Protein Homologies - Jaakkola, Diekhans, et al. - 2000
240	A new approach to protein fold recognition - Jones, Taylor, et al. - 1992
203	C.: Assignment of homology to genome sequences using a library of hidden markov models that represent all proteins of known structure - Gough, Karplus, et al. - 2001
176	Dominant forces in protein folding - Dill - 1990
176	A novel method of protein secondary structure prediction with high segment overlap measure: Support vector machine approach - Hua, Sun - 2001
152	Prediction of local structure in proteins using a library of sequence-structure motifs. - Bystroff, Baker - 1998
131	The Structural Alignment Between Two Proteins: Is there a Unique Answer?”, Protein Science 5:1325-1338, - Godzik - 1996
129	HMMSTR: A hidden Markov model for local sequence-structure correlations in proteins - Bystroff, Thorsson, et al.
124	Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments - Gotoh - 1996
99	Protein fold recognition using sequence-derived predictions - Fischer, Eisenberg - 1996
92	Structural design and molecular evolution of a cytokine receptor superfamily - Bazan - 1990
89	Protein secondary structure prediction with a neural network,” - Karplus - 1989
85	An analysis of recent work on clustering algorithms - Fasulo - 1999
80	Dynamic programming alignment accuracy. - Holmes, Durbin - 1998
78	Predicting protein structure using only sequence information. Proteins - Karplus, Barrett, et al. - 1999
77	Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. - Brevern, Etchebest, et al. - 2000
72	Solvation energy in protein folding and binding - Eisenberg, McLachlan - 1986
67	Dictionary of recurrent domains in protein structures. Proteins 33:88--96 - Holm, Sander - 1998
65	Protein Modeling using Hidden Markov Models: Analysis of Globins - Haussler, Krogh, et al. - 1993
58	Predicting reliable regions in protein sequence alignments. Bioinformatics - Cline, Hughey, et al. - 2002
57	Principles that determine the structure of proteins. - Chothia - 1984
54	A systematic comparison of protein structure classifications: Scop, cath and fssp - Hadley, Jones - 1999
51	Scoring Hidden Markov Models, - Barrett - 1997
46	Fully automated ab initio protein structure prediction using i-sites, hmmstr and rosetta - Bystroff, Shao - 2002
43	Artificial neural network model for predicting protein subcellular location. Comput Chem, - Cai, Liu, et al. - 2002
43	On the use of sequence homologies to predict protein structure: Identical pentapeptides can have completely different conformations. - Kabsch, Sander - 1984
42	Estimating the total number of protein folds. - Govindarajan, Recabarren, et al. - 1999
37	New methods for accurate prediction of protein secondary structure. Proteins - Chandonia, Karplus - 1999
37	Role of evolutionary information in predicting the disulfide-bonding state of cysteine in proteins - Fariselli, Riccobelli, et al. - 1999
36	Prediction of protein secondary structure by the hidden markov model - Asai, Hayamizu, et al. - 1993
34	Improving the quality of twilight-zone alignments - Jaroszewski, Rychlewski, et al. - 2000
33	1��6) A structural explanation for the twilight zone of protein sequence homology - Chung, Subbiah
31	Comparison of three algorithms for the assignment of secondary structure in proteins: The advantages of a consensus assignment. Protein Eng - Colloc’h, Etchebest, et al. - 1993
30	The PDBFINDER database: a summary of PDB, DSSP and HSSP information with added value. - RWW, Sander, et al. - 1996
29	Hidden markov models that use predicted secondary structures for fold recognition - Hargbo, Elofsson - 1999
28	Printing Office, - Abramowitz, A - 1964
27	Information-theoretic dissection of pairwise contact potentials - Cline, Karplus, et al. - 2002
22	Patterns, structures, and amino acid frequencies in structural building blocks, a protein secondary structure classification scheme. Proteins 27: 249–271 - Fetrow, Palumbo, et al. - 1997
21	The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs - Griffiths-Jones, Bateman
20	Protein fold recognition. - Jones, Thornton - 1993
19	Hidden Markov model approach for identifying the modular framework of the protein backbone. Protein Eng - Camproux, Tuffery, et al. - 1999
19	Rapid approximation to molecular surface area via the use of booleean logic look-up tables - Grand, Merz - 1993
19	Sequence alignment and modeling software system - SAM
18	Prediction of the number of residue contacts in proteins - Fariselli, Casadio - 2000
18	Protein topology recognition from secondary structure sequences: applications of the Hidden Markov Models to the alpha class proteins - FRANCESKO, GARNIER, et al. - 1997
17	The importance of larger data sets for protein secondary structure prediction with neural networks,” - Chandonia, Karplus - 1996
17	Anfinsen. Genetic control of tertiary protein structure - studies with model systems - Goldberger, B - 1963
16	Prediction of the transmembrane regions of beta barrel membrane proteins with a neural network based predictor. Protein Science 10 - Jacoboni, Martelli, et al. - 2001
15	Circular clustering of protein dihedral angles by minimum message length - Dowe, Allison, et al. - 1996
15	FORESST: fold recognition from secondary structure predictions of proteins. - Francesco, PJ, et al. - 1999
14	Excluded volume approximation to protein-solvent interaction. The solvent contact model. - Colonna-Cesari, Sander - 1990
14	Prediction of secondary structure by evolutionary comparison: Application to the a subunit of tryptophan synthase - Crawford, Niermann, et al. - 1987
13	Blind predictions of local protein structure in casp2 targets using the i-sites library - Bystroff, Baker - 1997
13	Fold recognition using predicted secondary structure sequences and hidden Markov models of protein folds - Francesco, Geetha, et al. - 1997
13	Fold recognition and ab initio structure predictions using hidden Markov models and b-strand pair potentials. Proteins - Hubbard, Park - 1995
10	Private communication - Cline - 1989
9	Protein Sequence Alignment Reliablity: Prediction and Measurement - Cline - 2000
7	Culling the PDB by resolution and sequence identity - Dunbrack - 2001
7	Estimation and use of protein backbone angle probabilities - Kang, Kurochkina, et al. - 1993
6	On the alignment shift and its measures - Cline, Karplus - 1998
6	Enzyme evolution explained (sort of - Dean, Golding - 2000
6	Casadio R. RCNPRED: prediction of the residue co-ordination numbers in proteins - Fariselli
6	G: Using information theory to discover side chain rotamer classes: analysis of the effects of local backbone structure. Pac Symp Biocomput - JS, Berg - 1999
6	A sentence to sentence clustering procedure for pattern analysis - Lu, Fu - 1978
6	A predicted consensus structure for the protein-kinase c2 homology (c2h) domain, the repeating unit of synaptotagmin. Proteins - DL, Chelvanayagam, et al. - 1995
5	Molecular surfaces: A review.http://www.netsci.org/science/compchem /feature14.html - Connolly - 1996
5	The protein fold of the von Willebrand factor type A domain is predicted to be similar to the open twisted beta-sheet flanked by alpha helices found in human Ras-p21 - Edwards, Perkins - 1995
3	Investigation of non-pairwise protein structure score functions using sets of decoy structures - Barrett - 2001
3	Factors limiting the performance of prediction-based fold recognition methods - Cruz, Thornton - 1999
3	Scoring functions for ab initio protein structure prediction - ES, Samudrala, et al.
2	A neural network predictor of residue contacts in proteins. Protein Engg - Fariselli, Casadio - 1999
2	Private communication - Karplus - 2000
1	Left-handed polypropline II helices commonly occur in globular proteins - Adzhubei, Sternberg - 1993
1	private communication - Czabaraka - 2003
1	class notes - Gregoret - 2000
1	A 4GL language - Hobbs - 1991