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Predict Protein

First-principles Methods for Predicting Protein Structure... [Pg.533]

Cuff IA and G J Barton 1999. Evaluation and Improvement of Multiple Sequence Methods for P Secondary Structure Prediction. Proteins Structure, Function and Genetics 34 508-519. [Pg.575]

The amount of computation necessary to try many conformers can be greatly reduced if a portion of the structure is known. One way to determine a portion of the structure experimentally is to obtain some of the internuclear distances from two-dimensional NMR experiments, as predicted by the nuclear Over-hauser effect (NOE). Once a set of distances are determined, they can be used as constraints within a conformation search. This has been particularly effective for predicting protein structure since it is very difficult to obtain crystallographic structures of proteins. It is also possible to define distance constraints based on the average bond lengths and angles, if we assume these are fairly rigid while all conformations are accessible. [Pg.185]

P Koehl, M Delarue. Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy. J Mol Biol 239 249-275, 1994. [Pg.308]

K Karplus, K Sjolander, C Barrett, M Cline, D Haussler, R Hughey, L Holm, C Sander. Predicting protein structure using hidden Markov models. Proteins Suppl 134-139, 1997. [Pg.345]

MAS Saqi, PA Bates, MJE Sternberg. Towards an automatic method of predicting protein structure by homology An evaluation of suboptimal sequence alignments. Protein Eng 5 305-311, 1992. [Pg.347]

D Eischer, D Eisenberg. Protein fold recognition using sequence-derived predictions. Protein Sci 5 947-955, 1996. [Pg.347]

B Rost, C Sander. Combining evolutionary information and neural networks to predict protein secondary stiaicture. Proteins Stiaict Fund Genet 19 55-72, 1994. [Pg.348]

JM Chandoma, M Karplus. Neural networks for secondary structure and structural class predictions. Protein Sci 4 275-285, 1995. [Pg.348]

P Stolorz, A Lapedes, Y Xia. Predicting protein secondary structure using neural net and statistical methods. J Mol Biol 225 363-377, 1992. [Pg.348]

Bonneau R, Tsai J, Ruczinski I, Chivian D, Rohl C, Strauss CEM, et al. Rosetta in CASP4 Progress in ab initio protein structure prediction. Proteins 2001 119-26. [Pg.351]

Gohlke H, Hendlich M, Klebe G. Knowledge-based scoring function to predict protein-ligand interactions. J Mol Biol 2000 295 337-56. [Pg.416]

A particular goal of chemical theory is to predict protein structure from the amino acid sequence—to calculate how polypeptides fold into the compact geometries of proteins. One strategy is to develop methods (often based on bioinformatics) for predicting structures approximately and then refining the structures... [Pg.76]

The ultimate goal of structural genomics is to provide a complete three-dimensional description of any gene product. Also, as the structures of more and more proteins of known function are elucidated, it should become increasingly possible to link specific functional attributes to specific structural attributes. As such, it may prove ultimately feasible to predict protein function if its structure is known, and vice versa. [Pg.65]

The term "structural genomics" is used to describe how the primary sequence of amino acids in a protein relates to the function of that protein. Currently, the core of structural genomics is protein structure determination, primarily by X-ray crystallography, and the design of computer programs to predict protein fold structures for new proteins based on their amino acid sequences and structural principles derived from those proteins whose 3-dimensional structures have been determined. Plant natural product pathways are a unique source of information for the structural biologist in view of the almost endless catalytic diversity encountered in the various pathway enzymes, but based on a finite number of reaction types. Plants are combinatorial chemists par excellence, and understanding the principles that relate enzyme structure to function will open up unlimited possibilities for the... [Pg.265]

MS instruments measure the mass-to-charge ratio (m/z) values of the smallest of molecules very accurately. In addition, the development of translated genomic databases and specialized software algorithms that rapidly search MS data against theoretical spectra of known or predicted proteins within databases is an important component that greatly facilitated the emergence of mass spectrometry-based proteomics as a key approach for large-scale proteomic analysis.15... [Pg.379]


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See also in sourсe #XX -- [ Pg.279 ]




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A Comparison of Protein Structure Prediction Methods CASP

Ab initio prediction of protein structure

All-atom protein structure prediction

Applications - Protein Structure Prediction

Automated ligand-protein docking prediction

Critical Assessment of Techniques for Protein Structure Prediction

Critical Assessment of Techniques for Protein Structure Prediction (CASP

Disordered proteins disorder prediction

First principles method for predicting protein

First-principles Methods for Predicting Protein Structure

Homologous proteins prediction

Knowledge-based prediction protein modeling

Learning for Protein Structure and Function Prediction

Molecular modeling protein structure prediction

Online protein structure prediction

Ordered proteins, amino acid sequence prediction

Predicting Protein Tertiary Structure

Prediction of Protein Secondary Structures from Sequences

Prediction of Secondary Structure in Proteins

Prediction of secondary and tertiary protein structure

Prediction techniques protein modeling

Prediction techniques test protein results

Predictions for Proteins with Known 3D Structure

Predictive methods using protein sequences

Protein Secondary Structure Prediction Suite

Protein Structure Prediction in ID, 2D, and

Protein antigenic sites location prediction

Protein folding class prediction

Protein folding predicted fold distribution

Protein folding quaternary structure prediction

Protein folding tertiary structure prediction

Protein function predictions

Protein loop prediction

Protein predictability

Protein predictability

Protein predicting

Protein predicting

Protein prediction

Protein prediction

Protein retention, predictability

Protein secondary structure prediction

Protein secondary structures predicting

Protein secondary structures structure prediction from

Protein sequence prediction

Protein sorting, subcellular localization prediction

Protein structure predicting

Protein structure prediction

Protein structure prediction approaches

Protein structure prediction from

Protein structure prediction from amino acid sequences

Protein tertiary structure prediction

Protein-based approach predicting functional sites

Proteins conformation prediction

Proteins stability prediction

Proteomics prediction of protein structures

Quaternary structure prediction, protein

Tertiary protein structure knowledge-based prediction

Tertiary protein structure predictions, derivation from

Testing for false positive predictions in membrane and soluble proteins of crystallographically known structure

Threading, predicting proteins

Understanding and Predicting Protein Structure

Unknown proteins, predicting functions

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