Search filters

List of works by Michael Nilges

1H, 15N, and 13C resonance assignment of the PH domain from C. elegans UNC-89

scientific article published in 1999

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

scientific article

A calculation strategy for the structure determination of symmetric dimers by 1H NMR.

scientific article published in November 1993

A comparison of the restrained molecular dynamics and distance geometry methods for determining three-dimensional structures of proteins on the basis of interproton distances

article

A convective replica‐exchange method for sampling new energy basins ⬇️

scientific article published on September 7, 2012

A model of the complex between single-stranded DNA and the single-stranded DNA binding protein encoded by gene V of filamentous bacteriophage M13.

scientific article published on July 1994

A new approach for applying residual dipolar couplings as restraints in structure elucidation

scientific article published in March 2000

A role for specific collagen motifs during wound healing and inflammatory response of fibroblasts in the teleost fish gilthead seabream.

scientific article

A simple method for delineating well-defined and variable regions in protein structures determined from interproton distance data

scholarly article by Michael Nilges published in July 1987

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

scientific article published in August 2008

A unifying probabilistic framework for analyzing residual dipolar couplings

scientific article published on 20 December 2007

ARIA2: automated NOE assignment and data integration in NMR structure calculation

scientific article

ARIA: automated NOE assignment and NMR structure calculation

scientific article (publication date: 22 January 2003)

ATP conformations and ion binding modes in the active site of anthrax edema factor: a computational analysis.

scientific article published in December 2009

Accurate NMR structures through minimization of an extended hybrid energy

scientific article published in September 2008

Ambiguous NOEs and automated NOE assignment

Ambiguous distance data in the calculation of NMR structures ⬇️

scientific article published on January 1, 1997

An Efficient Protocol for NMR-Spectroscopy-Based Structure Determination of Protein Complexes in Solution

scientific article published on 01 March 2010

An algorithm to enumerate all possible protein conformations verifying a set of distance constraints

scientific article

An automatic tool to analyze and cluster macromolecular conformations based on self-organizing maps

scientific article published on 26 December 2014

Application of the z-COSY technique with a modified pulse sequence to measurement of coupling constants in macromolecules

scholarly article by Hartmut Oschkinat et al published December 1987 in Journal of Magnetic Resonance

Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry

scientific article

Are there non-trivial dynamic cross-correlations in proteins? ⬇️

scientific article published on June 19, 1998

Assessing the quality of solution nuclear magnetic resonance structures by complete cross-validation.

scientific article published in July 1993

Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from beta-spectrin

scientific article

Automated structure modeling of large protein assemblies using crosslinks as distance restraints

scientific article

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

scientific article published in November 2005

Bayesian estimation of NMR restraint potential and weight: a validation on a representative set of protein structures

scientific article published in March 2011

Bayesian inference applied to macromolecular structure determination

scientific article

Biskit--a software platform for structural bioinformatics

scientific article

Blind testing of routine, fully automated determination of protein structures from NMR data

scientific article

Building Graphs To Describe Dynamics, Kinetics, and Energetics in the d-ALa:d-Lac Ligase VanA.

scientific article published on 31 August 2016

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

scientific article

Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulphide connectivities.

scientific article published in February 1995

Clinical and mutational investigations of tyrosinemia type II in Northern Tunisia: identification and structural characterization of two novel TAT mutations.

scientific article

Combining computational modeling with sparse and low-resolution data ⬇️

scientific article published on January 14, 2011

Comparative analysis of structural and dynamic properties of the loaded and unloaded hemophore HasA: functional implications

scientific article

Comparative evaluation of 3D virtual ligand screening methods: impact of the molecular alignment on enrichment

scientific article published in June 2010

Comparison of different torsion angle approaches for NMR structure determination.

scientific article published in March 2006

Complementarity of Structure Ensembles in Protein-Protein Binding

article published in 2004

Computational Reverse-Engineering of a Spider-Venom Derived Peptide Active Against Plasmodium falciparum SUB1 ⬇️

scientific article published on July 27, 2011

Computational approaches to the interpretation of NMR data for studying protein dynamics

article

Computational design of protein-based inhibitors of Plasmodium vivax subtilisin-like 1 protease

scientific article

Conformation of secretin in dimethyl sulfoxide solution. NMR studies and restrained molecular dynamics

scientific article

Conservation of the biochemical properties of IncA from Chlamydia trachomatis and Chlamydia caviae: oligomerization of IncA mediates interaction between facing membranes

scientific article published on 16 August 2004

Continuum solvent molecular dynamics study of flexibility in interleukin-8

article

Convective Replica-Exchange in Ergodic Regimes.

scientific article

Coronaviruses with a SARS-CoV-2-like receptor-binding domain allowing ACE2-mediated entry into human cells isolated from bats of Indochinese peninsula

Correction of spin diffusion during iterative automated NOE assignment

scientific article published in April 2004

Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

scientific article

Determination of the backbone conformation of secretin by restrained molecular dynamics on the basis of interproton distance data

scientific article

Determination of the three-dimensional solution structure of the C-terminal domain of cellobiohydrolase I from Trichoderma reesei. A study using nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing

scientific article

Determination of three-dimensional structures of proteins from interproton distance data by dynamical simulated annealing from a random array of atoms. Circumventing problems associated with folding

scientific article

Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry-dynamical simulated annealing calculations

scientific article

Discrimination of agonists versus antagonists of nicotinic ligands based on docking onto AChBP structures.

scientific article published on 29 June 2011

Distinct docking and stabilization steps of the Pseudopilus conformational transition path suggest rotational assembly of type IV pilus-like fibers

scientific article

Dynamics of a type 2 secretion system pseudopilus unraveled by complementary approaches

scientific article published on 23 May 2019

Efficient modeling of symmetric protein aggregates from NMR data

scientific article

Erratum: A convective replica-exchange method for sampling new energy basins

scholarly article published in Journal of Computational Chemistry

Error distribution derived NOE distance restraints.

scientific article published in August 2006

Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap ⬇️

scientific article published on June 1, 1998

Exploring protein interiors: the role of a buried histidine in the KH module fold

scientific article

Flexibility and conformational entropy in protein-protein binding

scientific article published on 01 April 2006

Floating stereospecific assignment revisited: application to an 18 kDa protein and comparison with J-coupling data

scientific article published on April 1, 1997

Functional analysis of early secreted antigenic target-6, the dominant T-cell antigen of Mycobacterium tuberculosis, reveals key residues involved in secretion, complex formation, virulence, and immunogenicity

scientific article published on 27 July 2005

Functional diversity of PH domains: an exhaustive modelling study ⬇️

scientific article published on January 1, 1997

Functional motions modulating VanA ligand binding unraveled by self-organizing maps.

scientific article published on 15 January 2014

Functionally important correlated motions in the single-stranded DNA-binding protein encoded by filamentous phage Pf3

scientific article published on 01 April 1999

Graphical analysis of NMR structural quality and interactive contact map of NOE assignments in ARIA

scientific article

Grid computing for improving conformational sampling in NMR structure calculation ⬇️

scientific article published on May 5, 2011

Heteronuclear relaxation study of the PH domain of beta-spectrin: restriction of loop motions upon binding inositol trisphosphate.

scientific article published in July 1998

ISD: a software package for Bayesian NMR structure calculation

scientific article published on 28 February 2008

Identification of binding sites and favorable ligand binding moieties by virtual screening and self-organizing map analysis

scientific article published on 21 March 2015

Identification of novel leishmanicidal molecules by virtual and biochemical screenings targeting Leishmania eukaryotic translation initiation factor 4A.

scientific article published on 18 January 2018

Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel

scientific article

Improved reliability, accuracy and quality in automated NMR structure calculation with ARIA.

scientific article published on 11 April 2015

Improved strategies for the determination of protein structures from NMR data: the solution structure of acyl carrier protein

scientific article

In Silico screening on the three-dimensional model of the Plasmodium vivax SUB1 protease leads to the validation of a novel anti-parasite compound

scientific article

Inferential Structure Determination of Chromosomes from Single-Cell Hi-C Data

scientific article (publication date: December 2016)

Inferential structure determination

scientific article published in July 2005

Influence of chemical shift tolerances on NMR structure calculations using ARIA protocols for assigning NOE data.

scientific article

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

scientific article

Influence of internal dynamics on accuracy of protein NMR structures: derivation of realistic model distance data from a long molecular dynamics trajectory.

scientific article

Insights into the enzymatic mechanism of 6-phosphogluconolactonase from Trypanosoma brucei using structural data and molecular dynamics simulation

scientific article

Internal repeats in the BRCA2 protein sequence

scientific article published in May 1996

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

scientific article

Modeling errors in NOE data with a log-normal distribution improves the quality of NMR structures

scientific article

Modeling pilus structures from sparse data.

scientific article

Modification in hydrophobic packing of HAMP domain induces a destabilization of the auto-phosphorylation site in the histidine kinase CpxA.

scientific article

Molecular replacement with NMR models using distance-derived pseudo B factors.

scientific article published on September 1996

NMR Exchange Format: a unified and open standard for representation of NMR restraint data

scientific article

NMR Relaxation Matrix Refinement of a DNA Octamer Solution Structure

NMR analysis of helix I from the 5S RNA of Escherichia coli

scientific article

NMR in the SPINE Structural Proteomics project.

scientific article

NMR studies of the sporulation protein SpoIIAA: implications for the regulation of the transcription factor sigmaF in Bacillus subtilis

scientific article published on 01 April 2001

Neisseria meningitidis Type IV Pili Composed of Sequence Invariable Pilins Are Masked by Multisite Glycosylation

scientific article published on 14 September 2015

Nicotine reverses hypofrontality in animal models of addiction and schizophrenia

scientific article published on 23 January 2017

Normal mode analysis suggests a quaternary twist model for the nicotinic receptor gating mechanism

scientific article

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

scientific article published on 18 June 2015

Pathways and intermediates in forced unfolding of spectrin repeats

scientific article published in August 2002

Posttranslational modification of pili upon cell contact triggers N. meningitidis dissemination

scientific article published on February 2011

Principal Component Analysis reveals correlation of cavities evolution and functional motions in proteins

scientific article published on 25 October 2014

Probabilistic Structure Calculation

Probabilistic structure calculation

Protein folding in mode space: a collective coordinate approach to structure prediction

scientific article

Quantitative study of the effects of chemical shift tolerances and rates of SA cooling on structure calculation from automatically assigned NOE data

scientific article

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

scientific article (publication date: June 2005)

Recommendations of the wwPDB NMR Validation Task Force

scientific article

Refined Structure, DNA Binding Studies, and Dynamics of the Bacteriophage Pf3 Encoded Single-Stranded DNA Binding Protein, ⬇️

scientific article published on July 29, 1997

Refined solution structure of the Tyr41-->His mutant of the M13 gene V protein. A comparison with the crystal structure

scientific article

Refinement of protein structures in explicit solvent

scientific article (publication date: 15 February 2003)

Refinement of the solution structure of the DNA decamer 5'd(CTGGATCCAG)2: combined use of nuclear magnetic resonance and restrained molecular dynamics

scientific article published on 01 June 1987

Relaxation matrix refinement of the solution structure of squash trypsin inhibitor

scientific article

Replica-Exchange Monte Carlo Scheme for Bayesian Data Analysis

scientific article published in Physical Review Letters

SAS profile correlations reveal SAS hierarchical nature and information content

scientific article

SAXS Merge: an automated statistical method to merge SAXS profiles using Gaussian processes

scientific article published on 14 December 2013

SNARE protein mimicry by an intracellular bacterium

scientific article

SOLARIA: A Protocol for Automated Cross-Peak Assignment and Structure Calculation for Solid-State Magic-Angle Spinning NMR Spectroscopy

scholarly article by Michele Fossi et al published 26 September 2005 in Angewandte Chemie International Edition

Sampling and efficiency of metric matrix distance geometry: a novel partial metrization algorithm

scientific article published in January 1992

Sequence-specific DNA binding activity of the cross-brace zinc finger motif of the piggyBac transposase

scientific article published on 27 January 2018

Sequential resonance assignment and secondary structure determination of the Ascaris trypsin inhibitor, a member of a novel class of proteinase inhibitors

article

Shelling the Voronoi interface of protein-protein complexes reveals patterns of residue conservation, dynamics, and composition.

scientific article published in August 2009

Solution structure of the 30 kDa polysulfide-sulfur transferase homodimer from Wolinella succinogenes

scientific article

Solution structure of the DNA-binding domain and model for the complex of multifunctional hexameric arginine repressor with DNA

scientific article

Solution structure of the coiled-coil trimerization domain from lung surfactant protein D

scientific article

Solution structure of the spectrin repeat: a left-handed antiparallel triple-helical coiled-coil

scientific article

StarDOM: from STAR format to XML.

scientific article published on October 1999

Structural Characterization of Whirlin Reveals an Unexpected and Dynamic Supramodule Conformation of Its PDZ Tandem

scientific article

Structural Insights into Serine-rich Fimbriae from Gram-positive Bacteria

scientific article

Structural and functional studies of titin’s fn3 modules reveal conserved surface patterns and binding to myosin S1 - a possible role in the frank-starling mechanism of the heart

article by Claudia Muhle-Goll et al published October 2001 in Journal of Molecular Biology

Structural biology by NMR: structure, dynamics, and interactions.

scientific article

Structural determination of Streptococcus pyogenes M1 protein interactions with human immunoglobulin G using integrative structural biology

scientific article published on 07 January 2021

Structure and function of minor pilins of type IV pili

scientific article published on 29 November 2019

Structure determination of the N-terminal thioredoxin-like domain of protein disulfide isomerase using multidimensional heteronuclear 13C/15N NMR spectroscopy

scientific article

Structure of Complement C3(H2O) Revealed By Quantitative Cross-Linking/Mass Spectrometry And Modeling

scientific article published on June 2016

Structure of a PH domain from the C. elegans muscle protein UNC-89 suggests a novel function

scientific article

Structure of the calcium-dependent type 2 secretion pseudopilus

scientific article published on 9 October 2017

Structure of the histone mRNA hairpin required for cell cycle regulation of histone gene expression

scientific article

Structure of the pleckstrin homology domain from beta-spectrin.

scientific article

Successful prediction of the coiled coil geometry of the GCN4 leucine zipper domain by simulated annealing: Comparison to the X-ray structure

scientific article published on 01 February 1993

Target Engagement and Binding Mode of an Antituberculosis Drug to Its Bacterial Target Deciphered in Whole Living Cells by NMR

scientific article published on 03 January 2019

Temperature Accelerated Molecular Dynamics with Soft-Ratcheting Criterion Orients Enhanced Sampling by Low-Resolution Information.

scientific article published on 3 June 2015

Tertiary structure prediction using mean-force potentials and internal energy functions: successful prediction for coiled-coil geometries

scientific article published on 01 January 1997

The dimerization stability of the HLH-LZ transcription protein family is modulated by the leucine zippers: a CD and NMR study of TFEB and c-Myc

scientific article published on 01 September 1994

The folding catalyst protein disulfide isomerase is constructed of active and inactive thioredoxin modules

scientific article published on 01 April 1997

The impact of protein flexibility on protein-protein docking

scientific article published on 01 January 2005

The leucine zippers of the HLH-LZ proteins Max and c-Myc preferentially form heterodimers

scientific article published on 01 October 1995

The redundancy of NMR restraints can be used to accelerate the unfolding behavior of an SH3 domain during molecular dynamics simulations

scientific article published on 24 November 2011

The solution structure of the Tyr41-->His mutant of the single-stranded DNA binding protein encoded by gene V of the filamentous bacteriophage M13.

scientific article

The solution structure of the first KH domain of FMR1, the protein responsible for the fragile X syndrome

scientific article

The structure in solution of the b domain of protein disulfide isomerase

scientific article

The three-dimensional structure of the HRDC domain and implications for the Werner and Bloom syndrome proteins

scientific article

Three dimensional structure and implications for the catalytic mechanism of 6-phosphogluconolactonase from Trypanosoma brucei

scientific article

Three-dimensional structure and stability of the KH domain: molecular insights into the fragile X syndrome

scientific article

Three-dimensional structure of acyl carrier protein in solution determined by nuclear magnetic resonance and the combined use of dynamical simulated annealing and distance geometry.

scientific article published in July 1988

Three-dimensional structure of phoratoxin in solution: combined use of nuclear magnetic resonance, distance geometry, and restrained molecular dynamics

article

Three-dimensional structure of potato carboxypeptidase inhibitor in solution. A study using nuclear magnetic resonance, distance geometry, and restrained molecular dynamics

article

Three-dimensional structure of the single-stranded DNA-binding protein encoded by gene V of the filamentous bacteriophage M13 and a model of its complex with single-stranded DNA

article

Toward a unified representation of protein structural dynamics in solution.

scientific article

Tuning interval Branch-and-Prune for protein structure determination

scholarly article by Bradley Worley et al published 9 March 2018 in Journal of Global Optimization

Visualization of macromolecular structures.

scientific article

Weighting of experimental evidence in macromolecular structure determination

scholarly article

mkgridXf: Consistent Identification of Plausible Binding Sites Despite the Elusive Nature of Cavities and Grooves in Protein Dynamics

scientific article published on 25 July 2019

Paulina is supported by:

About Paulina

Help