(Q46136198)

19 December 2017

title

Tools and databases to analyze protein flexibility; approaches to mapping implied features onto sequences (English)

1 reference

19 December 2017

author

Werner G. Krebs

1

1 reference

19 December 2017

Jochen Junker

4

1 reference

19 December 2017

Mark Bender Gerstein

6

object named as

Mark Gerstein

1 reference

19 December 2017

J Tsai

2

1 reference

19 December 2017

Vadim Alexandrov

3

1 reference

19 December 2017

Ronald Jansen

5

1 reference

19 December 2017

language of work or name

English

0 references

publication date

1 January 2003

1 reference

19 December 2017

published in

Methods in Enzymology

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19 December 2017

volume

374

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19 December 2017

page(s)

544-584

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19 December 2017

Steered molecular dynamics and mechanical functions of proteins

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Crystallographic refinement and atomic models of two different forms of citrate synthase at 2.7 and 1.7 A resolution

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7 January 2021

Glucose-induced conformational change in yeast hexokinase

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7 January 2021

Structural mechanisms for domain movements in proteins

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7 January 2021

Structural domains in proteins and their role in the dynamics of protein function

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7 January 2021

Refined crystal structure of dogfish M4 apo-lactate dehydrogenase

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7 January 2021

The crystal structure of the "open" and the "closed" conformation of the flexible loop of trypanosomal triosephosphate isomerase

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7 January 2021

Transmission of conformational change in insulin

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7 January 2021

An analysis of packing in the protein folding problem

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7 January 2021

Volume changes on protein folding.

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7 January 2021

Protein folding: the endgame

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7 January 2021

Calculation of molecular volumes and areas for structures of known geometry.

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Areas, volumes, packing and protein structure

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Determining the minimum number of types necessary to represent the sizes of protein atoms

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7 January 2021

Mechanisms of domain closure in proteins

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Elbow motion in the immunoglobulins involves a molecular ball-and-socket joint

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

GroEL/GroES: structure and function of a two-stroke folding machine

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Two-state allosteric behavior in a single-domain signaling protein

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Time-resolved x-ray diffraction reveals multiple conformations in the M-N transition of the bacteriorhodopsin photocycle

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Structure of a protein photocycle intermediate by millisecond time-resolved crystallography

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Time-resolved X-ray crystallographic study of the conformational change in Ha-Ras p21 protein on GTP hydrolysis

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Analysis of protein loop closure

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Average core structures and variability measures for protein families: application to the immunoglobulins

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Structure of haemoglobin: a three-dimensional Fourier synthesis at 5.5-A. resolution, obtained by X-ray analysis

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Structural comparisons of heme binding proteins

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

A systematic approach to the comparison of protein structures

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7 January 2021

Phosphocholine binding immunoglobulin Fab McPC603. An X-ray diffraction study at 2.7 A

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7 January 2021

Protein structure alignment

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7 January 2021

Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Detection of common three-dimensional substructures in proteins

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm.

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Structural alignment of globins, phycocyanins and colicin A.

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Optimum superimposition of protein structures: ambiguities and implications.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

A surface of minimum area metric for the structural comparison of proteins

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

1 reference

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7 January 2021

Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

A unified statistical framework for sequence comparison and structure comparison

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

An analysis of the three-dimensional structure of chicken triose phosphate isomerase

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Protein structure comparison by alignment of distance matrices

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

The limits of protein secondary structure prediction accuracy from multiple sequence alignment.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Multiple protein structure alignment

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

A flexible method to align large numbers of biological sequences.

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7 January 2021

Hierarchical method to align large numbers of biological sequences.

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7 January 2021

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7 January 2021

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7 January 2021

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7 January 2021

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7 January 2021

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7 January 2021

Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods

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7 January 2021

Anatomy of a conformational change: hinged "lid" motion of the triosephosphate isomerase loop.

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7 January 2021

Gating of the active site of triose phosphate isomerase: Brownian dynamics simulations of flexible peptide loops in the enzyme

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7 January 2021

Analysis of three human interleukin 5 structures suggests a possible receptor binding mechanism

1 reference

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7 January 2021

Pathways for proton release during ubihydroquinone oxidation by the bc(1) complex

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7 January 2021

Structure and function of the cytochrome bc1 complex of mitochondria and photosynthetic bacteria

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7 January 2021

Crystal structures of Escherichia coli glycerol kinase variant S58-->W in complex with nonhydrolyzable ATP analogues reveal a putative active conformation of the enzyme as a result of domain motion

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7 January 2021

Glycerol kinase from Escherichia coli and an Ala65-->Thr mutant: the crystal structures reveal conformational changes with implications for allosteric regulation

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7 January 2021

Aerosolized beclomethasone in chronic bronchitis. Improved pulmonary function and diminished airway inflammation

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7 January 2021

Plasma lactoferrin levels in pregnancy and cystic fibrosis

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7 January 2021

Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic

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7 January 2021

A dynamic model for the allosteric mechanism of GroEL

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7 January 2021

The allosteric mechanism of the chaperonin GroEL: a dynamic analysis

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Model-free methods of analyzing domain motions in proteins from simulation: a comparison of normal mode analysis and molecular dynamics simulation of lysozyme

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7 January 2021

Bending of the calmodulin central helix: a theoretical study

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Approximation and visualization of large-scale motion of protein surfaces

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7 January 2021

Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme

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7 January 2021

Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme

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7 January 2021

Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Computer simulations of macromolecular dynamics: models for vibrational spectroscopy and X-ray refinement

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Molecular dynamics of an alpha-helical polypeptide: Temperature dependence and deviation from harmonic behavior

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Enzyme specificity under dynamic control: a normal mode analysis of alpha-lytic protease

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Hinge-bending motion in citrate synthase arising from normal mode calculations.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Tertiary and quaternary conformational changes in aspartate transcarbamylase: a normal mode study

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Analysis of the low-frequency normal modes of the R state of aspartate transcarbamylase and a comparison with the T state modes

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Analysis of the low frequency normal modes of the T-state of aspartate transcarbamylase.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Analysis of domain motions by approximate normal mode calculations.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

The interpretation of protein structures: Total volume, group volume distributions and packing density

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

The packing density in proteins: standard radii and volumes.

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Calculations of protein volumes: sensitivity analysis and parameter database.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Calculation of protein volumes: an alternative to the Voronoi procedure

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Voronoi tessellation to study the numerical density and the spatial distribution of neurones.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Protein packing: dependence on protein size, secondary structure and amino acid composition.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Excluded volume in protein side-chain packing.

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Structure and dynamics of the fatty acid binding cavity in apo rat intestinal fatty acid binding protein

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Deviations from standard atomic volumes as a quality measure for protein crystal structures

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Accurate calculation of the density of proteins.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Statistical potentials extracted from protein structures: how accurate are they?

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Computer studies of interactions between macromolecules

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

The dynamics of proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Large-scale ab initio quantum chemical calculations on biological systems.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Time-trimming tricks for dynamic simulations: splitting force updates to reduce computational work.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

A structural census of genomes: comparing bacterial, eukaryotic, and archaeal genomes in terms of protein structure

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Patterns of protein-fold usage in eight microbial genomes: a comprehensive structural census

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Advances in structural genomics

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7 January 2021

The relationship between protein structure and function: a comprehensive survey with application to the yeast genome

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Annotation transfer for genomics: measuring functional divergence in multi-domain proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

SCOP: a Structural Classification of Proteins database

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Using CLUSTAL for multiple sequence alignments

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Pfam: multiple sequence alignments and HMM-profiles of protein domains

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Hidden Markov models in computational biology. Applications to protein modeling

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https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974023-3

7 January 2021

Maximum discrimination hidden Markov models of sequence consensus

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7 January 2021

Hidden Markov models of biological primary sequence information

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7 January 2021

The SWISS-PROT protein sequence data bank.

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7 January 2021

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7 January 2021

Protein superfamilies and domain superfolds

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7 January 2021

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7 January 2021

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Identifiers

DOI

1 reference

19 December 2017

PubMed ID

14696388

1 reference

19 December 2017