Protein structure modeling in the proteomics era. (Q30350916)

20 June 2017

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title

Protein structure modeling in the proteomics era. (English)

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20 June 2017

András Fiser

1

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20 June 2017

1 June 2004

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Expert Review of Proteomics

20 June 2017

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20 June 2017

1

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20 June 2017

97-110

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20 June 2017

1

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Plasticity of enzyme active sites

20 June 2017

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https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Evolution of function in protein superfamilies, from a structural perspective.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Core histones of the amitochondriate protist, Giardia lamblia.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Ligand-supported Homology Modelling of Protein Binding-sites using Knowledge-based Potentials

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

The distribution and query systems of the RCSB Protein Data Bank

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Evolution and physics in comparative protein structure modeling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Ab initio protein structure prediction: progress and prospects.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Recent improvements in prediction of protein structure by global optimization of a potential energy function.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Structure-based evaluation of sequence comparison and fold recognition alignment accuracy.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

One thousand families for the molecular biologist

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

SCOP: a structural classification of proteins database

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

The CATH Dictionary of Homologous Superfamilies (DHS): a consensus approach for identifying distant structural homologues.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Enhanced genome annotation using structural profiles in the program 3D-PSSM

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Advances in structural genomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

MODBASE, a database of annotated comparative protein structure models, and associated resources.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

The Protein Data Bank: unifying the archive

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Structural genomics: beyond the human genome project

21 January 2018

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https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Completeness in structural genomics.

21 January 2018

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https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Knowledge-based prediction of protein structures and the design of novel molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Knowledge-Based Protein Modeling

21 January 2018

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https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Comparative protein structure modeling of genes and genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Modeller: generation and refinement of homology-based protein structure models

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

GeneSilico protein structure prediction meta-server.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Critical assessment of methods of protein structure prediction (CASP)-round V.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Sequence alignment in molecular biology.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Large-scale comparison of protein sequence alignment algorithms with structure alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Hidden Markov models in computational biology. Applications to protein modeling

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Identification of sequence pattern with profile analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Fold prediction by a hierarchy of sequence, threading, and modeling methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Hidden Markov models for detecting remote protein homologies

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Detection of homologous proteins by an intermediate sequence search

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

A search for the most stable folds of protein chains

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional Structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Knowledge-based potentials for proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Evolutionary trees from DNA sequences: A maximum likelihood approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Recognition of errors in three-dimensional structures of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Large-scale protein structure modeling of the Saccharomyces cerevisiae genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Pairwise sequence alignment below the twilight zone

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Conserved key amino acid positions (CKAAPs) derived from the analysis of common substructures in proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Combining multiple structure and sequence alignments to improve sequence detection and alignment: application to the SH2 domains of Janus kinases

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Improving the quality of twilight-zone alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

A possible three-dimensional structure of bovine α-lactalbumin based on that of hen's egg-white lysozyme

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Comparative modeling methods: application to the family of the mammalian serine proteases

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Fragment ranking in modelling of protein structure. Conformationally constrained environmental amino acid substitution tables.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

An evaluation of the performance of an automated procedure for comparative modelling of protein tertiary structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

A 3D building blocks approach to analyzing and predicting structure of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Modelling the polypeptide backbone with 'spare parts' from known protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Database algorithm for generating protein backbone and side-chain co-ordinates from a C alpha trace application to model building and detection of co-ordinate errors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

A molecular dynamics approach for the generation of complete protein structures from limited coordinate data.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Accurate modeling of protein conformation by automatic segment matching

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

A new method for building protein conformations from sequence alignments with homologues of known structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Homology modelling by distance geometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

The PDB is a covering set of small protein structures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

From comparisons of protein sequences and structures to protein modelling and design

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Comparative protein modelling by satisfaction of spatial restraints

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Derivation of rules for comparative protein modeling from a database of protein structure alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Modeling of loops in protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Calculation of protein conformations by proton-proton distance constraints. A new efficient algorithm

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Application of molecular dynamics with interproton distance restraints to three-dimensional protein structure determination. A model study of crambin

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

An algorithm for determining the conformation of polypeptide segments in proteins by systematic search

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

PDB-based protein loop prediction: parameters for selection and methods for optimization.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

CODA: a combined algorithm for predicting the structurally variable regions of protein models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Conformations of immunoglobulin hypervariable regions

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Predicting the conformational class of short and medium size loops connecting regular secondary structures: application to comparative modelling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

An automated classification of the structure of protein loops.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Taxonomy and conformational analysis of loops in proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Comparison of systematic search and database methods for constructing segments of protein structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Have we seen all structures corresponding to short protein fragments in the Protein Data Bank? An update

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Modeling of protein loops by simulated annealing

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Development of an extended simulated annealing method: Application to the modeling of complementary determining regions of immunoglobulins

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Determining protein loop conformation using scaling-relaxation techniques

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Multiple copy sampling in protein loop modeling: computational efficiency and sensitivity to dihedral angle perturbations

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modelling

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

ModLoop: automated modeling of loops in protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

All-atom empirical potential for molecular modeling and dynamics studies of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Discrimination of native loop conformations in membrane proteins: decoy library design and evaluation of effective energy scoring functions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Solvation parameters for predicting the structure of surface loops in proteins: Transferability and entropic effects

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Analysis and prediction of inter-strand packing distances between beta-sheets of globular proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Crystal structure of the delta' subunit of the clamp-loader complex of E. coli DNA polymerase III

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Cell wall branches, penicillin resistance and the secrets of the MurM protein.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Comparative protein structure modeling by iterative alignment, model building and model assessment

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

In silico protein recombination: enhancing template and sequence alignment selection for comparative protein modelling

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Secondary structure formation in model polypeptide chains.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Compensating changes in protein multiple sequence alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Photoaffinity labeling approach to map the Taxol-binding site on the microtubule.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

From words to literature in structural proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Main-chain bond lengths and bond angles in protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Errors in protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

VERIFY3D: assessment of protein models with three-dimensional profiles

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

EVA: continuous automatic evaluation of protein structure prediction servers.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

LiveBench-1: continuous benchmarking of protein structure prediction servers

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Reliability of assessment of protein structure prediction methods.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Protein structure prediction and structural genomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Twilight zone of protein sequence alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Acuracy of refined protein structures. II. Comparison of four independently refined models of human interleukin 1beta.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Exploring the limits of precision and accuracy of protein structures determined by nuclear magnetic resonance spectroscopy.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

A mutant T4 lysozyme displays five different crystal conformations

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Probing the specificity of a trypanosomal aromatic alpha-hydroxy acid dehydrogenase by site-directed mutagenesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Convergent evolution of Trichomonas vaginalis lactate dehydrogenase from malate dehydrogenase

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Structure-based inhibitor design by using protein models for the development of antiparasitic agents

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Ligand specificity of brain lipid-binding protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Protein docking for low-resolution structures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Packaging of proteases and proteoglycans in the granules of mast cells and other hematopoietic cells. A cluster of histidines on mouse mast cell protease 7 regulates its binding to heparin serglycin proteoglycans

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Structure determination of turkey egg-white lysozyme using Laue diffraction data

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

A model for human cytochrome P450 2D6 based on homology modeling and NMR studies of substrate binding

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Crystal structure of a GCN5-related N-acetyltransferase: Serratia marcescens aminoglycoside 3-N-acetyltransferase

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Protein structure modeling for structural genomics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

MODBASE, a database of annotated comparative protein structure models

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

MODBASE, a database of annotated comparative protein structure models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Protein structures sustain evolutionary drift

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Conformation of β-hairpins in protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

A Structural Basis for Sequence Comparisons

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

Novel knowledge-based mean force potential at atomic level

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

1H, 13C, 15N resonance assignments and fold verification of a circular permuted variant of the potent HIV-inactivating protein cyanovirin-N

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2F14789450.1.1.97

21 January 2018

Identifiers

DOI

10.1586/14789450.1.1.97

1 reference

20 June 2017

1 reference

PubMed ID

15966803