Protein structure prediction: Recognition of primary, secondary, and tertiary structural features from amino acid sequence

Critical Reviews in Biochemistry and Molecular Biology

Volumn 30, Issue 1, 1995, Pages 1-94

  Eisenhaber, Frank ^a,b   Persson, Bengt ^b,c   Argos, Patrick ^b  

^a HUMBOLDT UNIVERSITY   (Germany)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^c KAROLINSKA INSTITUTE   (Sweden)

Author keywords

Conformational energy; Conformational search; Homology modeling; Prediction of secondary structural class; Prediction of transmembrane regions; Protein structure prediction; Reduced protein representation; Remotely related amino acid sequences; Secondary structure prediction; Sequence motif recognition; Side chain placement; Threading

Indexed keywords

ACYLPHOSPHATASE; MEMBRANE PROTEIN;

AMINO ACID SEQUENCE; CALCULATION; COMPUTER ANALYSIS; DATA BASE; ENERGY; HYDROPHOBICITY; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN LOCALIZATION; PROTEIN PROCESSING; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE; REVIEW; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; MATHEMATICS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROBABILITY; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SUPPORT, NON-U.S. GOV'T;

EID: 0028815464     PISSN: 10409238     EISSN: None     Source Type: Journal    
DOI: 10.3109/10409239509085139     Document Type: Article

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261. Protein folding classes: a geometric interpretation of the amino acid composition of globular proteins
262. Molecular dynamics simulation by atomic mass weighting
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264. Calculation of relative free energy via indirect pathways
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329. A comparison of alternative approaches to free energy calculations
330. Convex constraint analysis: a natural deconvolution of circular dichroism curves of proteins
331. Structures of N-terminally acetylated proteins
332. Prediction of trans-membrane regions in proteins utilising multiple sequence alignments
333. Evaluation of the sequence template method for protein structure prediction. Discrimination of the (beta/alpha) 8-barrel fold
334. Empirical scale of sidechain conformational entropy in protein folding
335. 2 synthase-1
336. The multiple-minima problem in the conformational analysis of molecules. Determination of the potential energy surface by the diffusion equation
337. Approximated potential functions of non-bonded interactions of methyl groups
338. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes
339. On α-helices terminated by glycine. I. Identification of common structural features
340. A segment-based approach to protein secondary structure prediction
341. Conversion from a virtual-bond chain to a complete polypeptide backbone
342. An approach to the multiple-minima problem in protein folding by relaxing dimensionality. Tests on enkephalin
343. Predicting the secondary structure of globular proteins using neural network models
344. A conformational preference parameter to predict helices in integral membrane proteins
345. Fold-class prediction by neural networks
346. The DEF data base of sequence based protein fold class predictions
347. A systematic approach to the comparison of protein structures
348. Myristylation and palmitylation of Src family members: the fats of the matter
349. Efficient algorithm for reconstruction of a protein backbone from the α-carbon coordinates
350. Emprical correlation between hydrophobic free energy and aqueous cavity surface area
351. Identification of structural motifs from protein coordinate data: secondary and first-level supersecondary structure
352. The anatomy and taxonomy of protein structure
353. Looking at proteins: representations, folding, packing, and design
354. Solvent accessible surface area and excluded volume in proteins
355. Taxonomy and conformational analysis of loops in proteins
356. On the multiple minima problem in the conformational analysis of polypeptides. V. Application of the self-consistent electrostatic field and the electrostatically driven Monte carlo methods to bovine pancreatic trypsin inhibitor
357. Relined models for computer calculations in protein engineering. Calibration and testing of atomic potential functions with ore efficient calculations
358. A fast, sensitive pattem-matching approach for protein sequences
359. Modeling side chains in peptides and proteins: application of the locally enhanced sampling and the simulated annealing methods to find minimum energy conformations
360. Prediction of protein backbone conformations based on seven structure assignments
361. Extracting information on folding from the amino acid sequence: accurate predictions for protein regions with preferred conformations in the absence of tertiary interactions
362. Identification of predictive sequence motifs limited by protein structure database size
363. A fast unbiased comparison of protein structures by means of the Needleman-Wunsch algorithm
364. Exploring structural homology of proteins
365. The taxonomy of protein structure
366. Redefining the goals of protein secondary structure prediction
367. Secondary structure prediction of all-helical proteins in two states
368. Combining evolutionary information and neural networks to predict protein secondary structure
369. Conservation and prediction of solvent accessibility in protein families
370. 1D secondary structure prediction through evolutionary Protiles
371. 9
372. A comparison of the CHARMM., AMBER and ECEPP potentials for peptides. II. phi-psi maps for N-acetyl alanine N'-methyl amide: comparisons, contrasts and simple experimental tests
373. Lagrangian molecular dynamics using selected conformational degrees of freedom, with application to pseudorotation dynamics of hose rings
374. Structure-based identification and clustering of protein farnilies and superfamilies
375. Structural features can be unconserved in proteins with similar folds. An analysis of side-chain to side-chain contacts, secondary structure and accessibility
376. Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels
377. The limits of protein secondary structure prediction accuracy from multiple sequence alignments
378. A geometrical constraint approach for reproducing the native backbone conformation of a protein
379. Kinetics of protein folding. A lattice model study of the requirements for folding to the native state
380. Definition of general topological equivalence in protein structures. A procedure involving comparison of prooperties and relationships through simulated annealing and dynamic programming
381. Comparative protein modeling by satisfaction of spatial restraints
382. Predicting protein secondary structure with a nearest-neighbor algorithm
383. Novel approach for computing the global minimum of proteins. I. General concepts, methods and approximations
384. Database of homol-ogy-derived protein structures and the structural meaning of sequence alignment
385. A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solutions
386. Prediction of homologous pre tein structures based on conformational searches and energetics
387. Inclusion of solvation free energy with molecular mechanics energy: alanyl dipeptide as test case
388. Protein structure prediction with a combined solvation free energy-molecular mechanics force field
389. Molecular dynamics with weighted time-averaged restraints for a DNA octamer
390. Rowers: to be or not to be? An analysis of amino acid sidechain conformations in globular proteins
391. Taming cut-off induced artefacts in molecular dynamics studies of solvated polypeptides
392. Low-frequency parametrization of hydrogen bonding
393. Multiple time steps: limits on the speedup of molecular dynamics simulations of aqueous systems
394. Application of the renormalization group to deterministic global minimization of molecular conformation energy functions
395. Amino acid composition and hydrophobicity patterns of protein domains correlate with their structures
396. Prediction of protein secondary stucture by a doublet code
397. High directional Monte Carlo procedure coupled with the temperature heating and annealing as a method to obtain the global energy minimum structure of polypeptides and proteins
398. Environment and exposure to solvent of protein atoms. Lysozyme and insulin
399. Conformation of beta-hairpins in protein structures: classifcation and diversity in homologous structures
400. Weighting aligned protein or nucleic acid sequences to correct for unequal representation
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402. Predicting the topology of eukaryotic membrane proteins
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405. Recognition of errors in threedimensional structures of proteins
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411. A novel method of protein sequence classification based on oligopeptide frequency analysis and its application to search for functional sites and to domain localization
412. A workbench for large-scale sequence homology analysis
413. The modular anangement of proteins as inferred from analysis of homology
414. Protein secondary structure from circular dichroism spec-troscopy
415. Evidence for disposable sequences inserted into a nucleotide fold
416. New spherical-cutoff methods for long-range forces in macromolecular simulation
417. Protein side-chain conformational entropy derived from fusion data-comparison with other empirical scales
418. Structural consequences of effector binding to the T state of aspartate carbamoyl-transferase: crystal structure of the unligated and ATP- and CTP-complexed enzymes at 2.6–Å resolution
419. Semianalytical treatment of solvation for molecular mechanics and dynamics
420. Defining to-pological equivalence in macromolecules
421. Construction of side-chains in homology modeling. Application to the C-terminal lobe of rhizopuspepsin
422. Reduced representation model pf protein structure prediction: statistical potential and genetic algorithm
423. Knowledge-based modeling of homologous proteins. II: Rules for conformations of substituted side chains
424. A study of structural determinants in the interleukin-1 fold
425. Medium and long-range interaction parameters between amino acids for predicting three-dimensional structure of proteins
426. Theory of protein titration curves. I. General equations for impenetrable spheres
427. Protein fold refinement: building models from idealized folds using motif constraints and multiple sequence data
428. A holistic approach to protein structure alignment
429. Protein structure alignment
430. Improved sensitivity of pfle searches through the use of sequence weights and gap excision
431. Protein threedimensional structure generation with an empirical hydrophobic penalty function
432. Fragment ranking in modeling of protein structure. Conformationally constrained environmental aminoacid substitution tables
433. Structural determinants of the conformations of medium-sized loops in proteins
434. Framework residue 71 is a major determinant of the position and conformation of the second hypervariable region in the V, domains of the immunoglobulins
435. A new approach to the rapid determination of protein side chain conformations
436. A critical comparison of search algorithms applied to the optimization of protein side-chain conformations
437. Molecular surface area and hydrophobic effect
438. Genetic algorithms for protein folding simulations
439. Finding the lowest free energy conformation is M NP-hard problem: proof and implications
440. Determining minimum energy confornations of polypeptides by dynamic programming
441. A molecular dynamics approach for the generation of complete protein structures from limited coordinate data
442. Algorithms for macromolecular dynamics and constraint dynamics
443. Computer simulation of molecular dynamics: methodology, application and perspectives in chemistry
444. A new family of powerful multivari-ate statistical sequence analysis (MSSA) techniques
445. A structure refinement method based on molecular dynamics in four spatial dimensions
446. Conformational search by potential energy annealing: algorithm and application to cyclosporin A
447. A Monte Carlo simulated annealing approach to optimization over continuous variables
448. Predicting immunoglobulin-like hypervariable loops
449. Use of buildup and energy minimization procedures to compute low-energy structures of the backbone of enkephalin
450. How transferable are hydrogen parameters in molecular mechanics calculations
451. Simple exact test for well-known molecular dynamics algorithms
452. Prediction of the folding pathways and the structure of the GNC4 leu-cine zipper
453. Empirical solvation models can be used to differentiate native from near-native conformations of bovine pancreatic trypsin inhibitor
454. Surface area included in energy refinement of proteins
455. Minimization of empirical energy functions including hydro-phobic surface area effects
456. The distribution of positively charged residues in bacterial inner membrane proteins correlates with trans-membrane topology
457. Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule
458. A combined iterative and boundary element approach for solution of the nonlinear Pois-son-Boltzmann equation
459. Prediction and analysis of structure, stability and unfolding of thermolysin-like proteases
460. Detection of common three-dimensional substructures in proteins
461. Quality control of protein models: directional atomic contact analysis
462. Use of amino acid environment-dependent substitution tables and conformational propensities in structure prediction from aligned sequences of homo-logues proteins. I. Solvent accessibility classes
463. Use of amino acid environment-dependent substitution tables and conformational propensities in structure prediction from aligned sequences of homologous proteins. II. Secondary structures
464. On the implementation of Friedman boundary conditions in liquid water simulations
465. A simplified amino acid potential for use in structure prediction of proteins
466. Electrostatic energy and macromolecular function
467. An all atom force field for simulations of proteons and nucleic acids
468. Structure of poM refined at 1.8 Å resolution
469. PROBIT. a statistical approach to modeling proteins from partial coordinate data using substructure libraries
470. Atomic solvation parameters applied to molecular dynamics of proteins in solution
471. Threedimensional Protiles from residue-pair preferences: identification of sequences with beta/alfa-barrel fold
472. Modeling side-chain conformation for homologous proteins using an energy-based rotamer search
473. Application of simulated annealing to peptides
474. A computer model to dynamically simulate protein folding: studies with crambin
475. Generating and testing protein folds
476. Sequences with 'unusual' amino acid compositions
477. Computing tertiary structures of proteins
478. Families and the structural relatedness among globular proteins
479. Protein structure prediction using nearest-neighbor methods
480. Calculations of a list of neighbors in molecular dynamics simulations
481. Monte Carlo simulation studies on the prediction of protein folding types from amino acid composition
482. An optimization approach to predicting protein structural class from amino acid composition
483. LIN: a new algorithm to simulate the dynamics of biomolecules by combining implicit-integration and normal mode techniques
484. The threedimensional Protile method using residue preference as a continuous function of residue environment
485. Entropic effects on disulfide bonds on protein stability
486. Hybrid system for protein secondary structure prediction
487. Loop closure via bond scaling and relaxation
488. Determining protein loop conformation using scaling-relaxation techniques
489. Multiple copy sampling: rigid versus flexible protein
490. Environment affects amino acid preference for secondary stmcture
491. ion of the protein secondary structure predictions
492. The alignment of protein structures in three dimensions