4.4 Review

Advances in automated NMR protein structure determination

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Direct visualization of secondary structures of F-actin by electron cryomicroscopy

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Predicting protein structures with a multiplayer online game

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Solid-state NMR and SAXS studies provide a structural basis for the activation of αB-crystallin oligomers

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Solution structure of the cap-independent translational enhancer and ribosome-binding element in the 3′ UTR of turnip crinkle virus

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Structure-oriented methods for protein NMR data analysis

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NMR in structural proteomics and beyond

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PICKY: a novel SVD-based NMR spectra peak picking method

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Automated assignment of NMR chemical shifts using peak-particle dynamics simulation with the DYNASSIGN algorithm

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De novo protein structure generation from incomplete chemical shift assignments

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TALOS plus : a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts

Yang Shen et al.

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Automated protein structure calculation from NMR data

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4D prediction of protein 1H chemical shifts

Juuso Lehtivarjo et al.

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Toward a Unified Representation of Protein Structural Dynamics in Solution

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Determination of Multicomponent Protein Structures in Solution Using Global Orientation and Shape Restraints

Jinbu Wang et al.

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Fast and Accurate Predictions of Protein NMR Chemical Shifts from Interatomic Distances

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NMR spectroscopy brings invisible protein states into focus

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CASD-NMR: critical assessment of automated structure determination by NMR

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Nature of the protein universe

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Characterization of protein secondary structure from NMR chemical shifts

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Automated NMR assignment and protein structure determination using sparse dipolar coupling constraints

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Improving NMR protein structure quality by Rosetta refinement: A molecular replacement study

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Influence of different assignment conditions on the determination of symmetric homodimeric structures with ARIA

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SAIL - stereo-array isotope labeling

Masatsune Kainosho et al.

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3D protein structures by solid-state NMR spectroscopy: Ready for high resolution

Anja Bockmann

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Macromolecular modeling with Rosetta

Rhiju Das et al.

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Contact replacement for NMR resonance assignment

Fei Xiong et al.

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ISD: a software package for Bayesian NMR structure calculation

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Recent progress and future directions in protein-protein docking

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Structural proteomics by NMR spectroscopy

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Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH

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Structure-based protein NMR assignments using native structural ensembles

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Sequence specific resonance assignment via Multicanonical Monte Carlo search using an ABACUS approach

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Automated amino acid side-chain NMR assignment of proteins using 13C- and 15N-resolved 3D [1H,1H]-NOESY

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A structure refinement protocol combining NMR residual dipolar couplings and small angle scattering restraints

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Assignment of protein NMR spectra based on projections, multi-way decomposition and a fast correlation approach

Doroteya K. Staykova et al.

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Solution NMR structure determination of proteins revisited

Martin Billeter et al.

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The war of tools: how can NMR spectroscopists detect errors in their structures?

E. Saccenti et al.

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Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data

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APSY-NMR with proteins: practical aspects and backbone assignment

Sebastian Hiller et al.

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Solution structure of the C-terminal dimerization domain of SARS coronavirus nucleocapsid protein solved by the SAIL-NMR method

Mitsuhiro Takeda et al.

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3D structure determination of the Crh protein from highly ambiguous solid-state NMR restraints

Antoine Loquet et al.

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Deuterated protein folds obtained directly from unassigned nuclear overhauser effect data

Guillermo A. Bermejo et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2008)

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Protein structure determination from 13C spin-diffusion solid-state NMR spectroscopy

Theofanis Manolikas et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2008)

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Biomolecular simulation and modelling: status, progress and prospects

Marc W. van der Kamp et al.

JOURNAL OF THE ROYAL SOCIETY INTERFACE (2008)

Article Biochemical Research Methods

NMR: prediction of molecular alignment from structure using the PALES software

Markus Zweckstetter

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CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data

David S. Wishart et al.

NUCLEIC ACIDS RESEARCH (2008)

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Paramagnetic shifts in solid-state NMR of proteins to elicit structural information

Stephane Balayssac et al.

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Consistent blind protein structure generation from NMR chemical shift data

Yang Shen et al.

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Stable isotope labeling methods for protein NMR spectroscopy

Shin-Ya Ohki et al.

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Determination of Protein Structures in the Solid State from NMR Chemical Shifts

Paul Robustelli et al.

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Phineus R. L. Markwick et al.

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A unifying probabilistic framework for analyzing residual dipolar couplings

Michael Habeck et al.

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Refined solution structure of the 82-kDa enzyme malate synthase G from joint NMR and synchrotron SAXS restraints

Alexander Grishaev et al.

JOURNAL OF BIOMOLECULAR NMR (2008)

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High-resolution structure prediction and the crystallographic phase problem

Bin Qian et al.

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Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology

Yang Shen et al.

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Building native protein conformation from NMR backbone chemical shifts using Monte Carlo fragment assembly

Haipeng Gong et al.

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Article Biochemistry & Molecular Biology

ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins

Markus Wiederstein et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Biochemical Research Methods

CISA: Combined NMR resonance connectivity information determination and sequential assignment

Xiang Wan et al.

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Protein structure determination from NMR chemical shifts

Andrea Cavalli et al.

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TAP score: torsion angle propensity normalization applied to local protein structure evaluation

Silvio C. E. Tosatto et al.

BMC BIOINFORMATICS (2007)

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Evaluating protein structures determined by structural genomics consortia

Aneerban Bhattacharya et al.

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RIKEN aids international structural genomics efforts

Shigeyuki Yokoyama et al.

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Automated structure determination of proteins with the SAIL-FLYA NMR method

Mitsuhiro Takeda et al.

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Fast high-resolution protein structure determination by using unassigned NMR data

Jegannath Korukottu et al.

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Article Biochemistry & Molecular Biology

Comparison of multiple amber force fields and development of improved protein backbone parameters

Viktor Hornak et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)

Article Chemistry, Multidisciplinary

Automated protein structure determination from NMR spectra

Blanca Lopez-Mendez et al.

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Solution NMR in structural genomics

Adelinda Yee et al.

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A polynomial-time algorithm for de novo protein backbone structure determination from nuclear magnetic resonance data

Lincong Wang et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2006)

Article Biochemistry & Molecular Biology

Inferential backbone assignment for sparse data

Olga Vitek et al.

JOURNAL OF BIOMOLECULAR NMR (2006)

Article Biochemistry & Molecular Biology

PREDITOR: a web server for predicting protein torsion angle restraints

Mark V. Berjanskii et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Biochemistry & Molecular Biology

HARMONY: a server for the assessment of protein structures

G. Pugalenthi et al.

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Evaluation of stereo-array isotope labeling (SAIL) patterns for automated structural analysis of proteins with CYANA

Teppei Ikeya et al.

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CRAACK: Consensus program for NMR amino acid type assignment

Cindy Benod et al.

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Using Xplor-NIH for NMR molecular structure determination

CD Schwieters et al.

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A method for evaluating the structural quality of protein models by using higher-order φ-ψ pairs scoring

GE Sims et al.

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Article Multidisciplinary Sciences

Optimal isotope labelling for NMR protein structure determinations

M Kainosho et al.

NATURE (2006)

Article Biochemical Research Methods

RIBRA - An error-tolerant algorithm for the NMR backbone assignment problem

KP Wu et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2006)

Article Biochemistry & Molecular Biology

A topology-constrained distance network algorithm for protein structure determination from NOESY data

YJ Huang et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)

Article Multidisciplinary Sciences

Weighting of experimental evidence in macromolecular structure determination

M Habeck et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Biochemical Research Methods

Traditional biomolecular structure determination by NMR spectroscopy allows for major errors

Sander B. Nabuurs et al.

PLOS COMPUTATIONAL BIOLOGY (2006)

Article Biochemical Research Methods

An efficient randomized algorithm for contact-based NMR backbone resonance assignment

H Kamisetty et al.

BIOINFORMATICS (2006)

Article Biochemistry & Molecular Biology

PASA - A program for automated protein NMR backbone signal assignment by pattern-filtering approach

YZ Xu et al.

JOURNAL OF BIOMOLECULAR NMR (2006)

Article Biochemistry & Molecular Biology

Solution structure of γS-crystallin by molecular fragment replacement NMR

ZR Wu et al.

PROTEIN SCIENCE (2005)

Article Biochemical Research Methods

The Victor/FRST function for model quality estimation

SCE Tosatto

JOURNAL OF COMPUTATIONAL BIOLOGY (2005)

Review Chemistry, Multidisciplinary

Scalable molecular dynamics with NAMD

JC Phillips et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)

Review Chemistry, Multidisciplinary

The GROMOS software for biomolecular simulation:: GROMOS05

M Christen et al.

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Review Chemistry, Multidisciplinary

The Amber biomolecular simulation programs

DA Case et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)

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Refinement of multidomain protein structures by combination of solution small-angle X-ray scattering and NMR data

A Grishaev et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)

Article Biochemical Research Methods

Bayesian estimation of Karplus parameters and torsion angles from three-bond scalar couplings constants

M Habeck et al.

JOURNAL OF MAGNETIC RESONANCE (2005)

Article Biochemistry & Molecular Biology

Automated protein NMR structure determination using wavelet de-noised NOESY spectra

F Dancea et al.

JOURNAL OF BIOMOLECULAR NMR (2005)

Article Multidisciplinary Sciences

Toward high-resolution de novo structure prediction for small proteins

P Bradley et al.

SCIENCE (2005)

Article Chemistry, Multidisciplinary

High-resolution iterative frequency identification for NMR as a general strategy for multidimensional data collection

HR Eghbalnia et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)

Article Multidisciplinary Sciences

Automated projection spectroscopy (APSY)

S Hiller et al.

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Article Multidisciplinary Sciences

Inferential structure determination

W Rieping et al.

SCIENCE (2005)

Article Biochemistry & Molecular Biology

Probabilistic identification of spin systems and their assignments including coil-helix inference as output (PISTACHIO)

HR Eghbalnia et al.

JOURNAL OF BIOMOLECULAR NMR (2005)

Article Biochemistry & Molecular Biology

The CCPN data model for NMR spectroscopy: Development of a software pipeline

WF Vranken et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)

Article Biochemistry & Molecular Biology

RECOORD:: A recalculated coordinate database of 500+proteins from the PDB using restraints from the BioMagResBank

AJ Nederveen et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)

Review Chemistry, Physical

High-throughput analysis of protein NMR spectra

D Malmodin et al.

PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY (2005)

Article Biochemical Research Methods

Periodicity, planarity, residual dipolar coupling, and structures

JD Walsh et al.

JOURNAL OF MAGNETIC RESONANCE (2005)

Review Biochemistry & Molecular Biology

Long-timescale simulation methods

R Elber

CURRENT OPINION IN STRUCTURAL BIOLOGY (2005)

Review Chemistry, Physical

Recent progress in the study of biomolecular structure and dynamics in solution from residual dipolar couplings

M Blackledge

PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY (2005)

Article Physics, Fluids & Plasmas

Bayesian inference applied to macromolecular structure determination

M Habeck et al.

PHYSICAL REVIEW E (2005)

Article Physics, Multidisciplinary

Replica-exchange Monte Carlo scheme for Bayesian data analysis

M Habeck et al.

PHYSICAL REVIEW LETTERS (2005)

Article Multidisciplinary Sciences

Simultaneous determination of protein structure and dynamics

K Lindorff-Larsen et al.

NATURE (2005)

Review Chemistry, Physical

Parallel tempering: Theory, applications, and new perspectives

DJ Earl et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2005)

Article Biochemistry & Molecular Biology

GANA - a genetic algorithm for NMR backbone resonance assignment

HN Lin et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Chemistry, Multidisciplinary

Local structure and anisotropic backbone dynamics from cross-correlated NMR relaxation in proteins

PRL Markwick et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2005)

Review Chemistry, Physical

Automated structure determination of proteins by NMR spectroscopy

W Gronwald et al.

PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY (2004)

Article Biochemical Research Methods

Correction of spin diffusion during iterative automated NOE assignment

JP Linge et al.

JOURNAL OF MAGNETIC RESONANCE (2004)

Article Chemistry, Multidisciplinary

Periodicity in residual dipolar couplings and nucleic acid structures

JD Walsh et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2004)

Review Cell Biology

The ABC's (and XYZ's) of peptide sequencing

H Steen et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2004)

Article Biochemistry & Molecular Biology

Mars - robust automatic backbone assignment of proteins

YS Jung et al.

JOURNAL OF BIOMOLECULAR NMR (2004)

Article Biochemistry & Molecular Biology

Backbone assignment of proteins with known structure using residual dipolar couplings

YS Jung et al.

JOURNAL OF BIOMOLECULAR NMR (2004)

Review Chemistry, Multidisciplinary

Residual dipolar couplings in structure determination of biomolecules

JH Prestegard et al.

CHEMICAL REVIEWS (2004)

Review Chemistry, Multidisciplinary

Automated analysis of protein NMR assignments and structures

MC Baran et al.

CHEMICAL REVIEWS (2004)

Review Chemistry, Physical

Validation of protein structures derived by NMR spectroscopy

CAEM Spronk et al.

PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY (2004)

Article Chemistry, Physical

Concepts and tools for NMR restraint analysis and validation

SB Nabuurs et al.

CONCEPTS IN MAGNETIC RESONANCE PART A (2004)

Article Biochemistry & Molecular Biology

BACUS: A Bayesian protocol for the identification of protein NOESY spectra via unassigned spin systems

A Grishaev et al.

JOURNAL OF BIOMOLECULAR NMR (2004)

Article Chemistry, Physical

Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules

D Hamelberg et al.

JOURNAL OF CHEMICAL PHYSICS (2004)

Article Biochemistry & Molecular Biology

Secondary structural effects on protein NMR chemical shifts'

YJ Wang

JOURNAL OF BIOMOLECULAR NMR (2004)

Article Chemistry, Multidisciplinary

Simultaneous assignment and structure determination of protein backbones by using NMR dipolar couplings

YS Jung et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2004)

Article Biochemistry & Molecular Biology

An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments

CJ Langmead et al.

JOURNAL OF BIOMOLECULAR NMR (2004)

Article Biochemical Research Methods

A polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments

CJ Langmead et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2004)

Article Biochemistry & Molecular Biology

DRESS: a database of REfined solution NMR structures

SB Nabuurs et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2004)

Review Chemistry, Multidisciplinary

Empirical force fields for biological macromolecules: Overview and issues

AD Mackerell

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)

Article Multidisciplinary Sciences

Rapid protein fold determination using unassigned NMR data

J Meiler et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)

Review Chemistry, Physical

Automated NMR protein structure calculation

P Güntert

PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY (2003)

Article Chemistry, Multidisciplinary

Theoretical analysis of residual dipolar coupling patterns in regular secondary structures of proteins

A Mascioni et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)

Article Chemistry, Multidisciplinary

Quantitative evaluation of experimental NMR restraints

SB Nabuurs et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)

Article Biochemistry & Molecular Biology

Fully automated sequence-specific resonance assignments of heteronuclear protein spectra

D Malmodin et al.

JOURNAL OF BIOMOLECULAR NMR (2003)

Article Biochemical Research Methods

Dipolar Waves as NMR maps of helices in proteins

MF Mesleh et al.

JOURNAL OF MAGNETIC RESONANCE (2003)

Article Biochemistry & Molecular Biology

Structure and dynamics of a membrane protein in micelles from three solution NMR experiments

S Lee et al.

JOURNAL OF BIOMOLECULAR NMR (2003)

Article Biochemistry & Molecular Biology

Effects of domain dissection on the folding and stability of the 43 kDa protein PGK probed by NMR

MAC Reed et al.

JOURNAL OF MOLECULAR BIOLOGY (2003)

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Dipolar waves map the structure and topology of helices in membrane proteins

MF Mesleh et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)

Article Biochemistry & Molecular Biology

Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts

S Neal et al.

JOURNAL OF BIOMOLECULAR NMR (2003)

Article Biochemistry & Molecular Biology

PACES: Protein sequential assignment by computer-assisted exhaustive search

BE Coggins et al.

JOURNAL OF BIOMOLECULAR NMR (2003)

Article Biochemistry & Molecular Biology

PROSHIFT: Protein chemical shift prediction using artificial neural networks

J Meiler

JOURNAL OF BIOMOLECULAR NMR (2003)

Article Biochemistry & Molecular Biology

Refinement of protein structures in explicit solvent

JP Linge et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2003)

Article Biochemistry & Molecular Biology

Structure validation by Cα geometry:: φ,ψ and Cβ deviation

SC Lovell et al.

PROTEINS-STRUCTURE FUNCTION AND GENETICS (2003)

Article Biochemistry & Molecular Biology

MONTE: An automated Monte Carlo based approach to nuclear magnetic resonance assignment of proteins

TK Hitchens et al.

JOURNAL OF BIOMOLECULAR NMR (2003)

Article Biochemical Research Methods

The Xplor-NIH NMR molecular structure determination package

CD Schwieters et al.

JOURNAL OF MAGNETIC RESONANCE (2003)

Article Biochemistry & Molecular Biology

Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS

T Herrmann et al.

JOURNAL OF BIOMOLECULAR NMR (2002)

Article Biochemistry & Molecular Biology

Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE)

W Gronwald et al.

JOURNAL OF BIOMOLECULAR NMR (2002)

Article Biochemical Research Methods

Assignment strategy for proteins with known structure

JC Hus et al.

JOURNAL OF MAGNETIC RESONANCE (2002)

Review Chemistry, Multidisciplinary

Molecular dynamics and NMR spin relaxation in proteins

DA Case

ACCOUNTS OF CHEMICAL RESEARCH (2002)

Article Multidisciplinary Sciences

CLOUDS, a protocol for deriving a molecular proton density via NMR

A Grishaev et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Article Multidisciplinary Sciences

Protein structure elucidation from NMR proton densities

A Grishaev et al.

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De novo determination of protein backbone structure from residual dipolar couplings using rosetta

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An NMR approach to structural proteomics

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The direct determination of protein structure by NMR without assignment

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Improving the quality of protein structures derived by NMR spectroscopy

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Protein backbone structure determination using only residual dipolar couplings from one ordering medium

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MUNIN: Application of three-way decomposition to the analysis of heteronuclear NMR relaxation data

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SANE (Structure assisted NOE evaluation): An automated model-based approach for NOE assignment

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Automatic determination of protein backbone resonance assignments from triple resonance nuclear magnetic resonance data

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Automated assignment of ambiguous nuclear overhauser effects with ARIA

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De novo protein structure determination using sparse NMR data

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Structural genomics projects in Japan

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Sequence-specific NMR assignment of proteins by global fragment mapping with the program MAPPER

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A tracked approach for automated NMR assignments in proteins (TATAPRO)

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RFAC, a program for automated NMR R-factor estimation

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Prediction of sterically induced alignment in a dilute liquid crystalline phase: Aid to protein structure determination by NMR

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The PSIPRED protein structure prediction server

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Protein structure determination using molecular fragment replacement and NMR dipolar couplings

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Point-centered domain decomposition for parallel molecular dynamics simulation

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The NOESY JIGSAW: Automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data

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The Protein Data Bank

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