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List of works by Volkhard Helms

A Brownian dynamics study: the effect of a membrane environment on an electron transfer system

scientific article

A STIM2 splice variant negatively regulates store-operated calcium entry.

scientific article published on 21 April 2015

A longer isoform of Stim1 is a negative SOCE regulator but increases cAMP-modulated NFAT signaling

scientific article published on 23 December 2021

A spatial model of the chromatophore vesicles of Rhodobacter sphaeroides and the position of the Cytochrome bc1 complex

scientific article published on 19 May 2006

A structural model of the complex formed by phospholamban and the calcium pump of sarcoplasmic reticulum obtained by molecular mechanics

scientific article published in December 2002

AKSmooth: enhancing low-coverage bisulfite sequencing data via kernel-based smoothing

scientific article

ALLO: a tool to discriminate and prioritize allosteric pockets.

scientific article published on 17 December 2017

AXER is an ATP/ADP exchanger in the membrane of the endoplasmic reticulum

scientific article published in Nature Communications

Adding phosphorylation events to the core oscillator driving the cell cycle of fission yeast

scientific article published in PLoS ONE

Adhesive water networks facilitate binding of protein interfaces

scientific article published in Nature Communications

Alternative binding modes of proline-rich peptides binding to the GYF domain

scientific article published in May 2005

An Update on Sec61 Channel Functions, Mechanisms, and Related Diseases.

scientific article published in November 2017

Are Solvation Free Energies of Homogeneous Helical Peptides Additive?

Assembly of transmembrane helices of simple polytopic membrane proteins from sequence conservation patterns

scientific article

Association of cytochrome c with membrane-bound cytochrome c oxidase proceeds parallel to the membrane rather than in bulk solution

scientific article published on March 2009

Atomistic simulation of water percolation and proton hopping in Nafion fuel cell membrane.

scientific article published in November 2010

Attraction within the membrane. Forces behind transmembrane protein folding and supramolecular complex assembly

scientific article

BEclear: Batch Effect Detection and Adjustment in DNA Methylation Data.

scientific article

Batch tautomer generation with MolTPC.

scientific article published on 2 August 2013

BiP-mediated closing of the Sec61 channel limits Ca2+ leakage from the ER

scientific article

BiP-mediated closing of the Sec61 channel limits Ca2+leakage from the ER

Bridging the gap: linking molecular simulations and systemic descriptions of cellular compartments

scientific article

Brownian dynamics simulations of simplified cytochrome c molecules in the presence of a charged surface

article

Bystander cells enhance NK cytotoxic efficiency by reducing search time

scientific article

Cellular functions of genetically imprinted genes in human and mouse as annotated in the gene ontology

scientific article

Classifying Substrate Specificities of Membrane Transporters fromArabidopsis thaliana

Coarse-grained Brownian dynamics simulations of protein translocation through nanopores

scientific article published in October 2012

Community-Associated Staphylococcus aureus from Sub-Saharan Africa and Germany: A Cross-Sectional Geographic Correlation Study

scientific article

Compact parameter set for fast estimation of proton transfer rates

Composition of Overlapping Protein-Protein and Protein-Ligand Interfaces

scientific article published on 30 October 2015

Computational Alchemy To Calculate Absolute Protein−Ligand Binding Free Energy

scientific article published in 1998

Conserved gating elements in TRPC4 and TRPC5 channels

scientific article published on 15 May 2013

Contribution of charged and polar residues for the formation of the E1-E2 heterodimer from Hepatitis C Virus

scientific article published on 2 March 2010

Contributors

Copy Number Alterations in Tumor Genomes Deleting Antineoplastic Drug Targets Partially Compensated by Complementary Amplifications

scientific article published on 01 September 2018

Cyclophilin A binds to linear peptide motifs containing a consensus that is present in many human proteins

scientific article published on 21 April 2005

DNA co-methylation analysis suggests novel functional associations between gene pairs in breast cancer samples

scientific article published on 09 April 2013

Design of a Gated Molecular Proton Channel

scholarly article by Wei Gu et al published 17 December 2010 in Angewandte Chemie International Edition

Designing binding pockets on protein surfaces using the A* algorithm

Detecting Staphylococcus aureus Virulence and Resistance Genes: a Comparison of Whole-Genome Sequencing and DNA Microarray Technology

scientific article published on 27 January 2016

Detection of Acidic Pharmaceutical Compounds Using Virus-Based Molecularly Imprinted Polymers.

scientific article published in September 2018

Determinants of ligand binding to cAMP-dependent protein kinase.

scientific article published on February 1999

Development of a high-throughput screening-compatible assay to identify inhibitors of the CK2α/CK2β interaction.

scientific article published on 16 September 2014

Different protonation equilibria of 4-methylimidazole and acetic acid

scientific article published in December 2007

Differential analysis of combinatorial protein complexes with CompleXChange.

scientific article

Diffusional encounter of barnase and barstar

scientific article published on 16 December 2005

Divergence of imprinted genes during mammalian evolution

scientific article

Downhill binding energy surface of the barnase-barstar complex.

scientific article published in November 2010

Druggability of dynamic protein-protein interfaces

scientific article published on January 2012

Dynamic Protonation Equilibrium of Solvated Acetic Acid

scholarly article by Wei Gu et al published 13 April 2007 in Angewandte Chemie International Edition

Dynamic water networks in cytochrome C oxidase from Paracoccus denitrificans investigated by molecular dynamics simulations

scientific article published on April 2004

Dynamical binding of proline-rich peptides to their recognition domains

scientific article

Dynamical properties of fasciculin-2.

scientific article published on September 1999

Dynamics of protein-protein encounter: a Langevin equation approach with reaction patches

scientific article published on October 2008

ENRI: A tool for selecting structure-based virtual screening target conformations

scientific article published on 20 December 2016

ER import of small human presecretory proteins: components and mechanisms

scientific article published on 29 July 2019

ERAD and protein import defects in a sec61 mutant lacking ER-lumenal loop 7.

scientific article

Eeyarestatin Compounds Selectively Enhance Sec61-Mediated Ca Leakage from the Endoplasmic Reticulum

scientific article published on 21 February 2019

Electronic excitations of biomolecules studied by quantum chemistry

scientific article

Elevated expression of the IGF2 mRNA binding protein 2 (IGF2BP2/IMP2) is linked to short survival and metastasis in esophageal adenocarcinoma

scientific article published on 06 July 2016

Elucidating the energetic contributions to the binding free energy.

scientific article published in January 2017

Energetics of Hydrophilic Protein–Protein Association and the Role of Water

Energetics of liposomes encapsulating silica nanoparticles

scientific article published on 24 February 2013

Energy barriers of proton transfer reactions between amino acid side chain analogs and water fromab initio calculations

Enthalpy-Entropy Compensation upon Molecular Conformational Changes

scientific article published on 11 March 2015

Expression regulation by a methyl-CpG binding domain in an E. coli based, cell-free TX-TL system.

scientific article published on 31 January 2017

Fatty acid elongation in non-alcoholic steatohepatitis and hepatocellular carcinoma

scientific article published on 4 April 2014

Free Energy Landscape of Protein-Protein Encounter Resulting from Brownian Dynamics Simulations of Barnase:Barstar

scientific article published in July 2005

Functional classification of membrane transporters and channels based on filtered TM/non-TM amino acid composition

article

Graph Measures Reveal Fine Structure of Complexes Forming in Multiparticle Simulations

article published in 2009

Graph-Based Clustering of Predicted Ligand-Binding Pockets on Protein Surfaces

scientific article

Graph-theoretical identification of dissociation pathways on free energy landscapes of biomolecular interaction

scientific article

Helical integrity and microsolvation of transmembrane domains from Flaviviridae envelope glycoproteins ⬇️

scientific article published on January 9, 2011

Hepatic hepcidin expression is decreased in cirrhosis and HCC

scientific article published on 21 November 2014

How Hydrophilic Proteins Form Nonspecific Complexes.

scientific article

How Molecular Conformational Changes Affect Changes in Free Energy

scientific article published in July 2015

How Peptides Bind to PSD-95/Discs-Large/ZO-1 Domains

scientific article published on 24 May 2022

How do proteins associate? A lesson from SH3 domain

article

How strongly do sequence conservation patterns and empirical scales correlate with exposure patterns of transmembrane helices of membrane proteins?

scientific article published on November 2006

How transient pockets open on the surface of the MDM2 protein

Human profilin 1 is a negative regulator of CTL mediated cell-killing and migration.

scientific article

Hydration energy landscape of the active site cavity in cytochrome P450cam

scientific article published on 01 August 1998

Hydration properties of natural and synthetic DNA sequences with methylated adenine or cytosine bases in the R.DpnI target and BDNF promoter studied by molecular dynamics simulations

scientific article published in December 2014

Hydrogen-bonded networks along and bifurcation of the E-pathway in quinol:fumarate reductase

scientific article

IMP2/p62 induces genomic instability and an aggressive hepatocellular carcinoma phenotype.

scientific article

Identification of key player genes in gene regulatory networks.

scientific article

Identification of novel diabetes impaired miRNA-transcription factor co-regulatory networks in bone marrow-derived Lin-/VEGF-R2+ endothelial progenitor cells

scientific article published on 11 July 2018

Identifying CpG islands by different computational techniques

scientific article published in April 2009

Identifying continuous pores in protein structures with PROPORES by computational repositioning of gating residues

scientific article published on 17 November 2011

Identifying transcription factor complexes and their roles

scientific article published on September 2014

Imprinted genes show unique patterns of sequence conservation

scientific article

Improved Binding of Cytochrome P450cam Substrate Analogues Designed To Fill Extra Space in the Substrate Binding Pocket†

article

Influence of key residues on the reaction mechanism of the cAMP-dependent protein kinase

scientific article published on December 1999

Integrative network-based approach identifies key genetic elements in breast invasive carcinoma

scientific article published on 26 May 2015

Interaction of calmodulin with Sec61α limits Ca2+ leakage from the endoplasmic reticulum

scientific article

Interfacing Brownian dynamics simulations

article

Interfering with Bacterial Quorum Sensing

scientific article published on 18 January 2016

Interorganelle Tethering to Endocytic Organelles Determines Directional Cytokine Transport in CD4+ T Cells

scientific article published on 26 October 2020

Ionic strength effects on the association funnel of barnase and barstar investigated by Brownian dynamics simulations

article

Kinase conformations: a computational study of the effect of ligand binding

scientific article published on November 1997

Lanthanum ions inhibit the mammalian Sec61 complex in its channel dynamics and protein transport activity

article

Linking Hematopoietic Differentiation to Co-Expressed Sets of Pluripotency-Associated and Imprinted Genes and to Regulatory microRNA-Transcription Factor Motifs

scientific article

Lipid Metabolism Signatures in NASH-Associated HCC--Letter

scientific article published on 28 April 2014

Low-lying electronic excitations of the green fluorescent protein chromophore

MINS2: revisiting the molecular code for transmembrane-helix recognition by the Sec61 translocon

scientific article

Matched-cohort DNA microarray diversity analysis of methicillin sensitive and methicillin resistant Staphylococcus aureus isolates from hospital admission patients

scientific article

Mechanism of fast peptide recognition by SH3 domains

scientific article

Mechanism of phosphoryl transfer in kinases investigated by semiempirical calculations

article published in 2003

Methylation-targeted specificity of the DNA binding proteins R.DpnI and MeCP2 studied by molecular dynamics simulations

scientific article published on 3 April 2017

Molecular dynamics of mouse acetylcholinesterase complexed with huperzine A.

scientific article published on October 1999

Molecular dynamics simulation of proton transport with quantum mechanically derived proton hopping rates (Q-HOP MD)

article

Molecular dynamics simulation of truncated bovine adrenodoxin

article

Molecular stochastic simulations of chromatophore vesicles from Rhodobacter sphaeroides

Monte Carlo simulation of biomolecular systems with BIOMCSIM

Multicopy molecular dynamics simulations suggest how to reconcile crystallographic and product formation data for camphor enantiomers bound to cytochrome P-450cam.

scientific article

Multistep mechanism of chloride translocation in a strongly anion-selective porin channel

scientific article published on August 2003

MutaNET: a tool for automated analysis of genomic mutations in gene regulatory networks

scientific article

NWChem: Past, present, and future

scientific article published on 01 May 2020

Novel scoring function for modeling structures of oligomers of transmembrane alpha-helices.

scientific article

On the derivation of propensity scales for predicting exposed transmembrane residues of helical membrane proteins

scientific article

Overexpression of IGF2 mRNA-Binding Protein 2 (IMP2/p62) as a Feature of Basal-like Breast Cancer Correlates with Short Survival.

scientific article published on August 2015

PPIXpress: construction of condition-specific protein interaction networks based on transcript expression

scientific article published on 27 October 2015

PRIMSIPLR: prediction of inner-membrane situated pore-lining residues for alpha-helical transmembrane proteins

scientific article published on 18 February 2014

Phosphoryl transfer by a concerted reaction mechanism in UMP/CMP-kinase

scientific article published on November 2000

Polyamines: naturally occurring small molecule modulators of electrostatic protein-protein interactions

scientific article published on 14 October 2009

PreTIS: A Tool to Predict Non-canonical 5' UTR Translational Initiation Sites in Human and Mouse

scientific article

Predicting Structural and Functional Properties of Membrane Proteins from Protein Sequence

Predicting the burial/exposure status of transmembrane residues in helical membrane proteins

Predicting where small molecules bind at protein-protein interfaces

scientific article

Prediction of the burial status of transmembrane residues of helical membrane proteins.

scientific article

Prediction of the exposure status of transmembrane beta barrel residues from protein sequence

scientific article

Prediction of the translocon-mediated membrane insertion free energies of protein sequences

scientific article published on 3 April 2008

Protein Dynamics Tightly Connected to the Dynamics of Surrounding and Internal Water Molecules

article

Protein translocation across the ER membrane

scientific article published on 27 June 2010

Protein transport into the human endoplasmic reticulum

scientific article published on 23 June 2014

Protein-protein docking of electron transfer complexes: Cytochromecoxidase and cytochromec

scholarly article by Dagmar Flöck published in February 2002

Protein–protein docking of electron transfer complexes: Cytochrome c oxidase and cytochrome c

scholarly article by Dagmar Flöck published in April 2002

Proteomic Analysis of the Initial Oral Pellicle in Caries-Active and Caries-Free Individuals

scientific article published on 19 December 2018

Proteomics reveals signal peptide features determining the client specificity in human TRAP-dependent ER protein import

scientific article published in Nature Communications

Proton shuttle in green fluorescent protein studied by dynamic simulations

scientific article

Putative cholesterol-binding sites in human immunodeficiency virus (HIV) coreceptors CXCR4 and CCR5.

scientific article published on 24 December 2012

Quantitative study of BSA coating silica nanoparticle

article published in 2014

Randomization Strategies Affect Motif Significance Analysis in TF-miRNA-Gene Regulatory Networks.

scientific article published on 4 July 2017

Re-face stereospecificity of methylenetetrahydromethanopterin and methylenetetrahydrofolate dehydrogenases is predetermined by intrinsic properties of the substrate

scientific article published in August 2001

Reaction rates for proton transfer over small barriers and connection to transition state theory

article published in 2001

Reconstruction of a kinetic model of the chromatophore vesicles from Rhodobacter sphaeroides ⬇️

scientific article published on 19 May 2006

Redox signals at the ER-mitochondria interface control melanoma progression

scientific article published on 15 July 2019

Relative Principal Components Analysis: Application to Analyzing Biomolecular Conformational Changes

scientific article published on 6 March 2019

Rewiring of the inferred protein interactome during blood development studied with the tool PPICompare.

scientific article

Rule-based regulatory and metabolic model for Quorum sensing in P. aeruginosa

scientific article

SNP and indel frequencies at transcription start sites and at canonical and alternative translation initiation sites in the human genome

scientific article published on 12 April 2019

Shedding light on the dark and weakly fluorescent states of green fluorescent proteins

scientific article published on May 1999

Specific and non-specific effects of potassium cations on substrate-protein interactions in cytochromes P450cam and P450lin

scientific article published in September 2002

Statistical analysis and exposure status classification of transmembrane beta barrel residues

scientific article

Statistical analysis of predominantly transient protein-protein interfaces

article

Structural changes in cytochrome P-450cam effected by the binding of the enantiomers (1R)-camphor and (1S)-camphor.

scientific article

TFmiR: a web server for constructing and analyzing disease-specific transcription factor and miRNA co-regulatory networks

scientific article published on 5 May 2015

TMBHMM: a frequency profile based HMM for predicting the topology of transmembrane beta barrel proteins and the exposure status of transmembrane residues

scientific article

TRAM1 protein may support ER protein import by modulating the phospholipid bilayer near the lateral gate of the Sec61-channel

scientific article published on 01 December 2020

Tandem repeats in the CpG islands of imprinted genes

article

The Mechanism of Proton Exclusion in the Aquaporin-1 Water Channel

scientific article published on 01 October 2003

The Regulation of the Calcium Signal by Membrane Pumps

scholarly article by Joachim Krebs et al published November 2003 in Helvetica Chimica Acta

The Role of Conformational Changes in Molecular Recognition

scientific article

The long non-coding RNA H19 suppresses carcinogenesis and chemoresistance in hepatocellular carcinoma

scientific article published on 25 August 2017

The mRNA-binding Protein TTP/ZFP36 in Hepatocarcinogenesis and Hepatocellular Carcinoma

scientific article published on 08 November 2019

The mechanism of phosphorylation of natural nucleosides and anti-HIV analogues by nucleoside diphosphate kinase is independent of their sugar substituents

scientific article published in July 2002

Thermodynamics of water mediating protein-ligand interactions in cytochrome P450cam: a molecular dynamics study

scientific article published on September 1995

Tightly Connected Water Wires Facilitate Fast Proton Uptake at The Proton Entrance of Proton Pumping Proteins

scientific article published in 2009

Titration behavior of residues at the entrance of the D-pathway of cytochrome c oxidase from paracoccus denitrificans investigated by continuum electrostatic calculations

scientific article published on October 2005

TopControl: A Tool to Prioritize Candidate Disease-associated Genes based on Topological Network Features

scientific article published on 19 December 2019

Topology Consistency of Disease-specific Differential Co-regulatory Networks

scientific article published on 06 November 2019

Transferring functional annotations of membrane transporters on the basis of sequence similarity and sequence motifs

scientific article

Transient Pockets on Protein Surfaces Involved in Protein−Protein Interaction

Transient pockets on XIAP-BIR2: toward the characterization of putative binding sites of small-molecule XIAP inhibitors

scientific article

Transport of soluble proteins through the Golgi occurs by diffusion via continuities across cisternae

scientific article

What induces pocket openings on protein surface patches involved in protein-protein interactions?

scientific article

Whole genome sequence typing and microarray profiling of nasal and blood stream methicillin-resistant Staphylococcus aureus isolates: Clues to phylogeny and invasiveness

scientific article published on 19 August 2015

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