Free energies of hydration from thermodynamic integration: Comparison of molecular mechanics force fields and evaluation of calculation accuracy. - Volkhard Helms; Rebecca C. Wade (J. Comput. Chem., 1997)

Conformational Transitions of Proteins from Atomistic Simulations. - Volkhard Helms; James Andrew McCammon (Computational Molecular Dynamics, 1999)

Energy barriers of proton transfer reactions between amino acid side chain analogs and water from ab initio calculations. - Elena Herzog; Tomaso Frigato; Volkhard Helms; C. Roy D. Lancaster (J. Comput. Chem., 2006)

QVADIS - a Package to Compute Proton Transfer Pathways in Proteins. - Kerstin Kunz; Volkhard Helms (German Conference on Bioinformatics, 2007)

On the derivation of propensity scales for predicting exposed transmembrane residues of helical membrane proteins. - Yungki Park; Volkhard Helms (Bioinform., 2007)

Prediction of the burial status of transmembrane residues of helical membrane proteins. - Yungki Park; Sikander Hayat; Volkhard Helms (BMC Bioinform., 2007)

The ABC (Analysing Biomolecular Contacts)-database. - Peter Walter; Sam Ansari; Volkhard Helms (J. Integr. Bioinform., 2007)

Designing Binding Pockets on Protein Surfaces using the A* Algorithm. - Susanne Eyrisch; Volkhard Helms (German Conference on Bioinformatics, 2008)

Prediction of the translocon-mediated membrane insertion free energies of protein sequences. - Yungki Park; Volkhard Helms (Bioinform., 2008)

MINS2: Revisiting the molecular code for transmembrane-helix recognition by the Sec61 translocon. - Yungki Park; Volkhard Helms (Bioinform., 2008)

What induces pocket openings on protein surface patches involved in protein-protein interactions? - Susanne Eyrisch; Volkhard Helms (J. Comput. Aided Mol. Des., 2009)

Graph-theoretical identification of dissociation pathways on free energy landscapes of biomolecular interaction. - Ling Wang; Boris Stumm; Volkhard Helms (J. Comput. Chem., 2010)

Classifying Substrate Specificities of Membrane Transporters from Arabidopsis thaliana. - Nadine S. Schaadt; Jan Christoph; Volkhard Helms (J. Chem. Inf. Model., 2010)

Statistical analysis and exposure status classification of transmembrane beta barrel residues. - Sikander Hayat; Yungki Park; Volkhard Helms (Comput. Biol. Chem., 2011)

Prediction of the Exposure Status of transmembrane beta Barrel residues from protein Sequence. - Sikander Hayat; Peter Walter; Yungki Park; Volkhard Helms (J. Bioinform. Comput. Biol., 2011)

Transferring functional annotations of membrane transporters on the basis of sequence similarity and sequence motifs. - Ahmad Barghash; Volkhard Helms (BMC Bioinform., 2013)

Rule-based regulatory and metabolic model for Quorum sensing in P. aeruginosa. - Nadine S. Schaadt; Anke Steinbach; Rolf W. Hartmann; Volkhard Helms (BMC Syst. Biol., 2013)

Batch tautomer generation with MolTPC. - Thorsten Will; Michael C. Hutter; Johann Jauch; Volkhard Helms (J. Comput. Chem., 2013)

Identifying transcription factor complexes and their roles. - Thorsten Will; Volkhard Helms (Bioinform., 2014)

AKSmooth: Enhancing low-coverage bisulfite sequencing data via kernel-based smoothing. - Junfang Chen; Pavlo Lutsik; Ruslan Akulenko; Jörn Walter; Volkhard Helms (J. Bioinform. Comput. Biol., 2014)

Graph-Based Clustering of Predicted Ligand-Binding Pockets on Protein Surfaces. - Jennifer Degac; Uwe Winter; Volkhard Helms (J. Chem. Inf. Model., 2015)

TFmiR: a web server for constructing and analyzing disease-specific transcription factor and miRNA co-regulatory networks. - Mohamed Hamed; Christian Spaniol; Maryam Nazarieh; Volkhard Helms (Nucleic Acids Res., 2015)

PPIXpress: construction of condition-specific protein interaction networks based on transcript expression. - Thorsten Will; Volkhard Helms (Bioinform., 2016)

Identification of key player genes in gene regulatory networks. - Maryam Nazarieh; Andreas Wiese; Thorsten Will; Mohamed Hamed; Volkhard Helms (BMC Syst. Biol., 2016)

PreTIS: A Tool to Predict Non-canonical 5' UTR Translational Initiation Sites in Human and Mouse. - Kerstin Reuter; Alexander Biehl; Laurena Koch; Volkhard Helms (PLoS Comput. Biol., 2016)

Rewiring of the inferred protein interactome during blood development studied with the tool PPICompare. - Thorsten Will; Volkhard Helms (BMC Syst. Biol., 2017)

Randomization Strategies Affect Motif Significance Analysis in TF-miRNA-Gene Regulatory Networks. - Sepideh Sadegh; Maryam Nazarieh; Christian Spaniol; Volkhard Helms (J. Integr. Bioinform., 2017)

MutaNET: a tool for automated analysis of genomic mutations in gene regulatory networks. - Markus Hollander; Mohamed Hamed; Volkhard Helms; Kerstin Neininger (Bioinform., 2018)

Topology Consistency of Disease-specific Differential Co-regulatory Networks. - Maryam Nazarieh; Hema Sekhar Reddy Rajula; Volkhard Helms (BMC Bioinform., 2019)

Differential analysis of combinatorial protein complexes with CompleXChange. - Thorsten Will; Volkhard Helms (BMC Bioinform., 2019)

TFmiR2: constructing and analyzing disease-, tissue- and process-specific transcription factor and microRNA co-regulatory networks. - Maryam Nazarieh; Mohamed Hamed; Christian Spaniol; Thorsten Will; Volkhard Helms (Bioinform., 2020)

Identification of Biomarkers Controlling Cell Fate In Blood Cell Development. - Maryam Nazarieh; Volkhard Helms; Marc P. Hoeppner; Andre Franke (CoRR, 2020)

Detecting Rewiring Events in Protein-Protein Interaction Networks Based on Transcriptomic Data. - Markus Hollander; Trang Do; Thorsten Will; Volkhard Helms (Frontiers Bioinform., 2021)

Identification of Biomarkers Controlling Cell Fate In Blood Cell Development. - Maryam Nazarieh; Marc P. Hoeppner; Volkhard Helms (Frontiers Bioinform., 2021)

ProPores2: Web Service and Stand-Alone Tool for Identifying, Manipulating, and Visualizing Pores in Protein Structures. - Markus Hollander; David J. N. P. Rasp; Moomal Aziz; Volkhard Helms (J. Chem. Inf. Model., 2021)

How does Sec63 affect the conformation of Sec61 in yeast? - Pratiti Bhadra; Lalitha Yadhanapudi; Karin Römisch; Volkhard Helms (PLoS Comput. Biol., 2021)

Optimized Data Set and Feature Construction for Substrate Prediction of Membrane Transporters. - Andreas Denger; Volkhard Helms (J. Chem. Inf. Model., 2022)