4.3 Article

CheSPI: chemical shift secondary structure population inference

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Multidisciplinary Sciences

ODiNPred: comprehensive prediction of protein order and disorder

Rupashree Dass et al.

SCIENTIFIC REPORTS (2020)

Article Biochemical Research Methods

A new clustering and nomenclature for beta turns derived from high-resolution protein structures

Maxim Shapovalov et al.

PLOS COMPUTATIONAL BIOLOGY (2019)

Article Multidisciplinary Sciences

Quality and bias of protein disorder predictors

Jakob T. Nielsen et al.

SCIENTIFIC REPORTS (2019)

Article Biochemistry & Molecular Biology

POTENCI: prediction of temperature, neighbor and pH-corrected chemical shifts for intrinsically disordered proteins

Jakob Toudahl Nielsen et al.

JOURNAL OF BIOMOLECULAR NMR (2018)

Article Multidisciplinary Sciences

Cryo-EM structures of tau filaments from Alzheimer's disease

Anthony W. P. Fitzpatrick et al.

NATURE (2017)

Article Biochemistry & Molecular Biology

Simultaneous quantification of protein order and disorder

Pietro Sormanni et al.

NATURE CHEMICAL BIOLOGY (2017)

Article Endocrinology & Metabolism

PCA as a Practical Indicator of OPLS-DA Model Reliability

Bradley Worley et al.

CURRENT METABOLOMICS (2016)

Article Biochemistry & Molecular Biology

There is Diversity in Disorder -In all Chaos there is a Cosmos, in all Disorder a Secret Order

Jakob T. Nielsen et al.

FRONTIERS IN MOLECULAR BIOSCIENCES (2016)

Article Biochemistry & Molecular Biology

CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts

Noor E. Hafsa et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Multidisciplinary Sciences

Heterogeneous binding of the SH3 client protein to the DnaK molecular chaperone

Jung Ho Lee et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Review Biochemistry & Molecular Biology

Computational approaches for inferring the functions of intrinsically disordered proteins

Mihaly Varadi et al.

FRONTIERS IN MOLECULAR BIOSCIENCES (2015)

Article Biochemistry & Molecular Biology

pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins

Mihaly Varadi et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemistry & Molecular Biology

Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks

Yang Shen et al.

JOURNAL OF BIOMOLECULAR NMR (2013)

Article Chemistry, Physical

Replica-Averaged Metadynamics

Carlo Camilloni et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Review Biochemistry & Molecular Biology

Polyproline-II Helix in Proteins: Structure and Function

Alexei A. Adzhubei et al.

JOURNAL OF MOLECULAR BIOLOGY (2013)

Article Biochemistry & Molecular Biology

Using NMR chemical shifts to calculate the propensity for structural order and disorder in proteins

Kamil Tamiola et al.

BIOCHEMICAL SOCIETY TRANSACTIONS (2012)

Article Chemistry, Multidisciplinary

Mapping the Potential Energy Landscape of Intrinsically Disordered Proteins at Amino Acid Resolution

Valery Ozenne et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2012)

Article Chemistry, Multidisciplinary

Interpreting Protein Structural Dynamics from NMR Chemical Shifts

Paul Robustelli et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2012)

Article Chemistry, Multidisciplinary

β-Sheet Core of Tau Paired Helical Filaments Revealed by Solid-State NMR

Venita Daebel et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2012)

Article Biochemical Research Methods

Template-based protein structure modeling using the RaptorX web server

Morten Kaellberg et al.

NATURE PROTOCOLS (2012)

Review Chemistry, Physical

Disordered proteins studied by chemical shifts

Magnus Kjaergaard et al.

PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY (2012)

Review Chemistry, Physical

Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field

Jakob T. Nielsen et al.

PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY (2012)

Article Biochemistry & Molecular Biology

Ensemble modeling of protein disordered states: Experimental restraint contributions and validation

Joseph A. Marsh et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2012)

Article Medicine, Research & Experimental

α-Synuclein in Parkinson's Disease

Leonidas Stefanis

COLD SPRING HARBOR PERSPECTIVES IN MEDICINE (2012)

Article Biochemistry & Molecular Biology

Random coil chemical shift for intrinsically disordered proteins: effects of temperature and pH

Magnus Kjaergaard et al.

JOURNAL OF BIOMOLECULAR NMR (2011)

Article Biochemical Research Methods

Protein 8-class secondary structure prediction using conditional neural fields

Zhiyong Wang et al.

PROTEOMICS (2011)

Review Neurosciences

SOD1 Transcriptional and Posttranscriptional Regulation and Its Potential Implications in ALS

Pamela Milani et al.

NEUROLOGY RESEARCH INTERNATIONAL (2011)

Article Biochemistry & Molecular Biology

Rapid Communication: Cu/Zn Superoxide Dismutase Activity in Familial and Sporadic Amyotrophic Lateral Sclerosis

Wim Robberecht et al.

JOURNAL OF NEUROCHEMISTRY (2010)

Article Chemistry, Multidisciplinary

A Combinatorial NMR and EPR Approach for Evaluating the Structural Ensemble of Partially Folded Proteins

Jampani Nageswara Rao et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2010)

Article Chemistry, Multidisciplinary

Defining Conformational Ensembles of Intrinsically Disordered and Partially Folded Proteins Directly from Chemical Shifts

Malene Ringkjobing Jensen et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2010)

Article Chemistry, Multidisciplinary

Sequence-Specific Random Coil Chemical Shifts of Intrinsically Disordered Proteins

Kamil Tamiola et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2010)

Article Biochemistry & Molecular Biology

Effect of Pseudorepeat Rearrangement on α-Synuclein Misfolding, Vesicle Binding, and Micelle Binding

Jampani Nageswara Rao et al.

JOURNAL OF MOLECULAR BIOLOGY (2009)

Article Chemistry, Multidisciplinary

Accurate Random Coil Chemical Shifts from an Analysis of Loop Regions in Native States of Proteins

Alfonso De Simone et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2009)

Article Multidisciplinary Sciences

Transient structural distortion of metal-free Cu/Zn superoxide dismutase triggers aberrant oligomerization

Kaare Teilum et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Review Chemistry, Physical

Characterization of protein secondary structure from NMR chemical shifts

Steven P. Mielke et al.

PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY (2009)

Article Biochemistry & Molecular Biology

Characterization of α-synuclein interactions with selected aggregation-inhibiting small molecules

Jampani Nageswara Rao et al.

BIOCHEMISTRY (2008)

Article Chemistry, Multidisciplinary

X-ray structure of snow flea antifreeze protein determined by racemic crystallization of synthetic protein enantiomers

Brad L. Pentelute et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2008)

Article Biochemistry & Molecular Biology

The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts

Mark V. Berjanskii et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Multidisciplinary Sciences

Protein structure determination from NMR chemical shifts

Andrea Cavalli et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Biochemistry & Molecular Biology

2DCSi: identification of protein secondary structure and redox state using 2D cluster analysis of NMR chemical shifts

Ching-Cheng Wang et al.

JOURNAL OF BIOMOLECULAR NMR (2007)

Article Chemistry, Multidisciplinary

Highly populated turn conformations in natively unfolded Tau protein identified from residual dipolar couplings and molecular simulation

Marco D. Mukrasch et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2007)

Review Biochemistry & Molecular Biology

Structure, folding, and misfolding of Cu,Zn superoxide dismutase in amyotrophic lateral sclerosis

Rishi Rakhit et al.

BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE (2006)

Article Automation & Control Systems

OPLS discriminant analysis:: combining the strengths of PLS-DA and SIMCA classification

Max Bylesjo et al.

JOURNAL OF CHEMOMETRICS (2006)

Review Chemistry, Multidisciplinary

Conformation of the backbone in unfolded proteins

Zhengshuang Shi et al.

CHEMICAL REVIEWS (2006)

Article Biochemistry & Molecular Biology

Structural and mechanistic insights into ras association domains of phospholipase C epsilon

TD Bunney et al.

MOLECULAR CELL (2006)

Article Multidisciplinary Sciences

Polyproline II conformation is one of many local conformational states and is not an overall conformation of unfolded peptides and proteins

J Makowska et al.

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

Article Multidisciplinary Sciences

A structural model for unfolded proteins from residual dipolar couplings and small-angle x-ray scattering

P Bernadó et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Multidisciplinary Sciences

Glycine-rich antifreeze proteins from snow fleas

LA Graham et al.

SCIENCE (2005)

Article Multidisciplinary Sciences

Statistical coil model of the unfolded state: Resolving the reconciliation problem

AK Jha et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Clinical Neurology

Alpha-Synuclein dysfunction in Lewy body diseases

GK Tofaris et al.

MOVEMENT DISORDERS (2005)

Article Multidisciplinary Sciences

α-synuclein locus triplication causes Parkinson's disease

AB Singleton et al.

SCIENCE (2003)

Article Multidisciplinary Sciences

Tau filaments from human brain and from in vitro assembly of recombinant protein show cross-β structure

J Berriman et al.

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

Article Biochemistry & Molecular Biology

Prediction algorithm for amino acid types with their secondary structure in proteins (PLATON) using chemical shifts

D Labudde et al.

JOURNAL OF BIOMOLECULAR NMR (2003)

Article Biochemistry & Molecular Biology

The solution structure of reduced dimeric copper zinc superoxide dismutase - The structural effects of dimerization

L Banci et al.

EUROPEAN JOURNAL OF BIOCHEMISTRY (2002)

Article Multidisciplinary Sciences

Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation

JS Richardson et al.

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

Article Automation & Control Systems

Orthogonal projections to latent structures (O-PLS)

J Trygg et al.

JOURNAL OF CHEMOMETRICS (2002)

Article Chemistry, Multidisciplinary

Sequence-dependent correction of random coil NMR chemical shifts

S Schwarzinger et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2001)

Article Multidisciplinary Sciences

Assembly of τ protein into Alzheimer paired helical filaments depends on a local sequence motif (306VQIVYK311) forming β structure

M von Bergen et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2000)