Structural Bioinformatics Group

Publications of AG Preissner

Editorial responsibility by Robert Preissner.
The open access documents can be downloaded as pdf files for personal academic use.
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2018

Pain-prescription differences - an analysis of 500,000 discharge summaries
and
In Current Drug Abuse Reviews, Sep
.

Exploring Activity Profiles of PAINS and Their Structural Context in Target-Ligand Complexes

In Journal of Chemical Information and Modeling, Aug
, IF: 3.804.

Prediction Is a Balancing Act: Importance of Sampling Methods to Balance Sensitivity and Specificity of Predictive Models Based on Imbalanced Chemical Data Sets
, and
In Frontiers in Chemistry Volume 6, 362, Aug
, IF: 4.155.

Molecular basis for the sensitivity of TRP channels to polyunsaturated fatty acids
and
In Naunyn-Schmiedeberg's Archives of Pharmacology, May
, IF: 2.558.

The Catch-22 of Predicting hERG Blockade Using Publicly Accessible Bioactivity Data
and
In Journal of Chemical Information and Modeling, May
, IF: 3.76.

ProTox-II: a webserver for the prediction of toxicity of chemicals
, , and
In Nucleic Acids Research, Apr
, IF: 10.162.

BitterSweetForest: A Random Forest Based Binary Classifier to Predict Bitterness and Sweetness of Chemical Compounds
and
In Frontiers in Chemistry Volume 6, 93, Apr
, IF: 3.994.

WITHDRAWN – A One-stop Source for Drug Withdrawals
and
In pharmazeutische medizin Volume 20, 38-43, Mar
.

Suppressive Effects of Clerodendrum volubile P Beauv. [Labiatae] Methanolic Extract and Its Fractions on Type 2 Diabetes and Its Complications
, , , , , , , , , and
In Frontiers in Pharmacology Volume 9, 8, Feb
, IF: 4.4.

Computational and experimental validation of antioxidant properties of synthesized bioactive ferulic acid derivatives
, , , , , and
In International Journal of Food Properties Volume 21, 86-98, Feb
, IF: 1.427.

mVOC 2.0: a database of microbial volatiles
, , , , and
In Nucleic Acids Res. Volume 46, D1261-D1265, Jan
, IF: 10.162.

SuperDRUG2: a one stop resource for approved/marketed drugs
, , , , , , and
In Nucleic Acids Res. Volume 46, D1137-D1143, Jan
, IF: 10.162.

2017

The target landscape of clinical kinase drugs
, , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , and
In Science Volume 358, Dec
, IF: 37.205.

Volatile Organic Compounds in the Breath of Oral Squamous Cell Carcinoma Patients: A Pilot Study
, , , , and
In Otolaryngol Head Neck Surg Volume 157, 981–987, Dec
, IF: 2.021.

Computational prediction of immune cell cytotoxicity
, , , , , and
In Food Chem. Toxicol. Volume 107, 150–166, Sep
, IF: 3.584.

Drugs as habitable planets in the space of dark chemical matter
and
In Drug Discov. Today, Jul
, IF: 6.369.

Statin and rottlerin small-molecule inhibitors restrict colon cancer progression and metastasis via MACC1
, , , , , , , , , , , , and
In PLoS Biol. Volume 15, e2000784, Jun
, IF: 8.668.

Volatile organic compounds in the breath of oral candidiasis patients: a pilot study
, , , , , , and
In Clin Oral Investig, Jun
, IF: 2.207.

Bax/Bak-independent mitochondrial depolarization and reactive oxygen species induction by sorafenib overcome resistance to apoptosis in renal cell carcinoma
, , , , , and
In J. Biol. Chem. Volume 292, 6478–6492, April
, IF: 4.573.

CardioScape mapping the cardiovascular funding landscape in Europe
, , , , , , , , and
In Eur. Heart J., Apr
, IF: 20.212.

Anti-diabetic effect of the ethyl acetate fraction of Clerodendrum volubile: protocatechuic acid suppresses phagocytic oxidative burst and modulates inflammatory cytokines
, , , , , , , , and
In Biomed. Pharmacother. Volume 86, 307–315, Feb
, IF: 2.326.

2016

TRPC6 G757D Loss-of-Function Mutation Associates with FSGS
, , , , , , , , , , , , , and
In J. Am. Soc. Nephrol. Volume 27, 2771–2783, Sep
, IF: 9.343.

Computational methods for prediction of in vitro effects of new chemical structures
, , and
In J Cheminform Volume 8, 51, Sep
, IF: 3.949.

Adjuvant antifungal therapy using tissue tolerable plasma on oral mucosa and removable dentures in oral candidiasis patients: a randomised double-blinded split-mouth pilot study
, , , , , , and
In Mycoses Volume 59, 467–475, Jul
, IF: 2.239.

SL2: an interactive webtool for modeling of missing segments in proteins
, , , , and
In Nucleic Acids Res. Volume 44, W390–394, Jul
, IF: 9.202.

Chemical Proteomics Reveals Ferrochelatase as a Common Off-target of Kinase Inhibitors
, , , , , , , , , , , , and
In ACS Chem. Biol. Volume 11, 1245–1254, May
, IF: 5.331.

Inhibition of DNA-Topoisomerase I by Acylated Triterpene Saponins from Pittosporum angustifolium Lodd
, , and
In Nat Prod Bioprospect Volume 6, 141–147, Apr
.

Detection of signature volatiles for cariogenic microorganisms
, , , , and
In Eur. J. Clin. Microbiol. Infect. Dis. Volume 35, 235–244, Feb
, IF: 2.67.

Identification of signature volatiles to discriminate Candida albicans, glabrata, krusei and tropicalis using gas chromatography and mass spectrometry
, , , , , , , and
In Mycoses Volume 59, 117–126, Feb
, IF: 2.24.

WITHDRAWN–a resource for withdrawn and discontinued drugs
, , , , and
In Nucleic Acids Res. Volume 44, D1080–1086, Jan
, IF: 9.11.

CancerResource–updated database of cancer-relevant proteins, mutations and interacting drugs
, , , and
In Nucleic Acids Res. Volume 44, D932–937, Jan
, IF: 9.11.

eGender-from e-Learning to e-Research: a web-based interactive knowledge-sharing platform for sex- and gender-specific medical education
, , , , , and
In Biol Sex Differ Volume 7, 3,
, IF: 3.635.

2015

DBEndo: a web-based endodontic case management tool
, , , , and
In BMC Res Notes Volume 8, 685, Nov
.

2D and 3D similarity landscape analysis identifies PARP as a novel off-target for the drug Vatalanib
, , , , , and
In BMC Bioinformatics Volume 16, 308, Sep
, IF: 2.58.

Molecular similarity-based predictions of the Tox21 screening outcome
and
In Front. Environ. Sci. Volume 3, 54, Jul
.

Super Natural II–a database of natural products
, , , , and
In Nucleic Acids Res. Volume 43, D935–939, Jan
, IF: 8.81.

Acyclovir Has Low but Detectable Influence on HLA-B*57:01 Specificity without Inducing Hypersensitivity
, , , , , , , , , , , , , , and
In PLoS ONE Volume 10, e0124878,
, IF: 4.411.

Personalized Cancer Therapy Considering Cytochrome P450 Variability
, , and
In Adv. Pharmacol. Volume 74, 113–130,
.

2014

ProTox: a web server for the in silico prediction of rodent oral toxicity
, , , and
In Nucleic Acids Res. Volume 42, W53–58, Jul
, IF: 8.026.

SuperPred: update on drug classification and target prediction
, , , , , , and
In Nucleic Acids Res. Volume 42, 26–31, Jul
, IF: 8.026.

mVOC: a database of microbial volatiles
, , , and
In Nucleic Acids Res. Volume 42, D744–748, Jan
, IF: 8.026.

The Transformer database: biotransformation of xenobiotics
, , , , and
In Nucleic Acids Res. Volume 42, D1113–1117, Jan
, IF: 8.026.

SuperPain–a resource on pain-relieving compounds targeting ion channels
, and
In Nucleic Acids Res. Volume 42, D1107–1112, Jan
, IF: 8.026.

GenderMedDB: an interactive database of sex and gender-specific medical literature
, , , and
In Biol Sex Differ Volume 5, 7,
, IF: 3.237.

2013

Residues of a proposed gate region in type I ATP-binding cassette import systems are crucial for function as revealed by mutational analysis
, , , , , , , and
In Biochim. Biophys. Acta Volume 1828, 2164–2172, Sep
, IF: 3.99.

Targeted therapy of the XIAP/proteasome pathway overcomes TRAIL-resistance in carcinoma by switching apoptosis signaling to a Bax/Bak-independent 'type I' mode
, , , , , , , and
In Cell Death Dis Volume 4, e643, May
, IF: 5.333.

VaccImm: simulating peptide vaccination in cancer therapy
, , and
In BMC Bioinformatics Volume 14, 127, Apr
, IF: 3.02.

Mapping discontinuous protein-binding sites via structure-based peptide libraries: combining in silico and in vitro approaches
, , , , , , , , and
In J. Mol. Recognit. Volume 26, 23–31, Jan
, IF: 3.31.

SynSysNet: integration of experimental data on synaptic protein-protein interactions with drug-target relations
, , , , , , , , , , , , , and
In Nucleic Acids Res. Volume 41, D834–840, Jan
, IF: 8.026.

A new algorithm for integrated analysis of miRNA-mRNA interactions based on individual classification reveals insights into bladder cancer
, , , , and
In PLoS ONE Volume 8, e64543,
, IF: 4.411.

Polymorphic cytochrome P450 enzymes (CYPs) and their role in personalized therapy
, , , , and
In PLoS ONE Volume 8, e82562,
, IF: 4.411.

2012

Binding sites in membrane proteins–diversity, druggability and prospects
, , , , and
In Eur. J. Cell Biol. Volume 91, 326–339, Apr
, IF: 3.63.

SuperTarget goes quantitative: update on drug-target interactions
, , , , , , , and
In Nucleic Acids Res. Volume 40, D1113–1117, Jan
, IF: 7.836.

Drug cocktail optimization in chemotherapy of cancer
, , , , , , and
In PLoS ONE Volume 7, e51020,
, IF: 4.411.

2011

SDM–a server for predicting effects of mutations on protein stability and malfunction
, and
In Nucleic Acids Res. Volume 39, W215–222, Jul
, IF: 7.836.

Cobweb: a Java applet for network exploration and visualisation
, and
In Bioinformatics Volume 27, 1725–1726, Jun
, IF: 4.926.

PROMISCUOUS: a database for network-based drug-repositioning
, , , , and
In Nucleic Acids Res. Volume 39, D1060–1066, Jan
, IF: 7.836.

FragmentStore–a comprehensive database of fragments linking metabolites, toxic molecules and drugs
, , , , , and
In Nucleic Acids Res. Volume 39, D1049–1054, Jan
.

SuperSweet–a resource on natural and artificial sweetening agents
, , , , and
In Nucleic Acids Res. Volume 39, D377–382, Jan
.

CancerResource: a comprehensive database of cancer-relevant proteins and compound interactions supported by experimental knowledge
, , , , , , , and
In Nucleic Acids Res. Volume 39, D960–967, Jan
.

Development of immune-specific interaction potentials and their application in the multi-agent-system VaccImm
, , , , and
In PLoS ONE Volume 6, e23257,
.

2010

Analysis of sex and gender-specific research reveals a common increase in publications and marked differences between disciplines
, , , and
In BMC Med Volume 8, 70, Nov
, IF: 3.99.

Novel compounds with antiangiogenic and antiproliferative potency for growth control of testicular germ cell tumours
, , , , , , , and
In Br. J. Cancer Volume 103, 18–28, Jun
, IF: 4.346.

Endogenous Bak inhibitors Mcl-1 and Bcl-xL: differential impact on TRAIL resistance in Bax-deficient carcinoma
, , , , , , , , , and
In J. Cell Biol. Volume 188, 851–862, Mar
, IF: 9.12.

Enzymatic, expression and structural divergences among carboxyl O-methyltransferases after gene duplication and speciation in Nicotiana
, , , , and
In Plant Mol. Biol. Volume 72, 311–330, Feb
, IF: 3.541.

Structural features and evolution of protein-protein interactions
, and
In Genome Inform Volume 22, 1–10, Jan
, IF: 3.609.

SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions
, , , , , , , , and
In Nucleic Acids Res. Volume 38, D237–243, Jan
, IF: 6.954.

Theoretical modeling techniques and their impact on tumor immunology
, and
In Clin. Dev. Immunol. Volume 2010, 271794,
, IF: 3.0.

DNA vaccination: using the patient's immune system to overcome cancer
, , , and
In Clin. Dev. Immunol. Volume 2010, 169484,
, IF: 3.0.

2009

Computer-assisted identification of small-molecule Bcl-2 modulators
, , , and
In Comput Biol Chem Volume 33, 451–456, Dec
, IF: 1.837.

Inhibiting the inhibitors: retro-inverso Smac peptides
, , , , and
In Peptides Volume 30, 2374–2379, Dec
, IF: 2.565.

Cellular fingerprints: a novel approach using large-scale cancer cell line data for the identification of potential anticancer agents
, , , and
In Chem Biol Drug Des Volume 74, 439–448, Nov
.

SuperLooper–a prediction server for the modeling of loops in globular and membrane proteins
, , , , , and
In Nucleic Acids Res. Volume 37, W571–574, Jul
, IF: 6.954.

Survivin minigene DNA vaccination is effective against neuroblastoma
, , , , , , , , , , , , , and
In Int. J. Cancer Volume 125, 104–114, Jul
, IF: 4.555.

SuperToxic: a comprehensive database of toxic compounds
, , , , , , , and
In Nucleic Acids Res. Volume 37, D295–299, Jan
, IF: 6.954.

JAIL: a structure-based interface library for macromolecules
, , and
In Nucleic Acids Res. Volume 37, D338–341, Jan
, IF: 6.954.

SuperSite: dictionary of metabolite and drug binding sites in proteins
, , , , and
In Nucleic Acids Res. Volume 37, 195–200, Jan
, IF: 6.954.

Voronoia: analyzing packing in protein structures
, , , and
In Nucleic Acids Res. Volume 37, D393–395, Jan
, IF: 6.954.

SuperScent–a database of flavors and scents
, , , , , , , , , , and
In Nucleic Acids Res. Volume 37, D291–294, Jan
, IF: 6.954.

2008

Notch inhibition blocks multiple myeloma cell-induced osteoclast activation
, , , , , , , and
In Leukemia Volume 22, 2273–2277, Dec
, IF: 6.924.

A rationally designed tyrosine hydroxylase DNA vaccine induces specific antineuroblastoma immunity
, , , , , , and
In Mol. Cancer Ther. Volume 7, 2241–2251, Jul
, IF: 5.137.

Superimpose: a 3D structural superposition server
, , , , , , , , , , , and
In Nucleic Acids Res. Volume 36, 47–54, Jul
, IF: 6.954.

SuperPred: drug classification and target prediction
, , , and
In Nucleic Acids Res. Volume 36, W55–59, Jul
, IF: 6.954.

Hydrogen-bonding and packing features of membrane proteins: functional implications
, , , , and
In Biophys. J. Volume 94, 1945–1953, Mar
, IF: 4.757.

SuperTarget and Matador: resources for exploring drug-target relationships
, , , , , , , , , , , , , , and
In Nucleic Acids Res. Volume 36, D919–922, Jan
, IF: 6.954.

Comparative VEGF receptor tyrosine kinase modeling for the development of highly specific inhibitors of tumor angiogenesis
, , , and
In Genome Inform Volume 20, 243–251,
.

Suffix techniques as a rapid method for RNA substructure search
, , and
In Genome Inform Volume 20, 183–198,
.

Toxicity versus potency: elucidation of toxicity properties discriminating between toxins, drugs, and natural compounds
, , , , and
In Genome Inform Volume 20, 231–242,
.

2007

Docking without docking: ISEARCH–prediction of interactions using known interfaces
, , , and
In Proteins Volume 69, 839–844, Dec
, IF: 3.73.

SuperHapten: a comprehensive database for small immunogenic compounds
, , , and
In Nucleic Acids Res. Volume 35, D906–910, Jan
.

A structural genomics approach to the regulation of apoptosis: chimp vs. human
, , and
In Genome Inform Volume 18, 22–34,
.

2006

Characterization of GD2 peptide mimotope DNA vaccines effective against spontaneous neuroblastoma metastases
, , , , , , , , , , , , , , and
In Cancer Res. Volume 66, 10567–10575, Nov
, IF: 7.616.

Legionella pneumophila induces IFNbeta in lung epithelial cells via IPS-1 and IRF3, which also control bacterial replication
, , , , , , , , , , , , and
In J. Biol. Chem. Volume 281, 36173–36179, Nov
.

Analysis and prediction of helix-helix interactions in membrane channels and transporters
, , and
In Proteins Volume 64, 253–262, Jul
, IF: 4.684.

Photoactivation of an inhibitor of the 12/15-lipoxygenase pathway
, , , , , , and
In Chembiochem Volume 7, 1089–1095, Jul
, IF: 3.94.

Natural products: sources and databases
, , and
In Nat Prod Rep Volume 23, 347–356, Jun
, IF: 7.89.

Representation of target-bound drugs by computed conformers: implications for conformational libraries
, , , and
In BMC Bioinformatics Volume 7, 293, Jun
, IF: 5.423.

SuperMimic–fitting peptide mimetics into protein structures
, , and
In BMC Bioinformatics Volume 7, 11, Jan
, IF: 5.423.

SuperNatural: a searchable database of available natural compounds
, , and
In Nucleic Acids Res. Volume 34, D678–683, Jan
, IF: 7.552.

Design and biological evaluation of photo-switchable inhibitors
, , , , , and
In Genome Inform Volume 17, 141–151,
.

2005

SUPERFICIAL–surface mapping of proteins via structure-based peptide library design
, and
In BMC Bioinformatics Volume 6, 223, Sep
, IF: 5.423.

Novel curcumin- and emodin-related compounds identified by in silico 2D/3D conformer screening induce apoptosis in tumor cells
, , , , and
In BMC Cancer Volume 5, 97, Aug
, IF: 2.293.

SuperLigands - a database of ligand structures derived from the Protein Data Bank
, , and
In BMC Bioinformatics Volume 6, 122, May
, IF: 5.423.

In silico screening of drug databases for TSE inhibitors
, and
In BioSystems Volume 80, 117–122, May
, IF: 1.144.

SuperDrug: a conformational drug database
, , , and
In Bioinformatics Volume 21, 1751–1753, May
, IF: 6.701.

Molecular packing and packing defects in helical membrane proteins
, , , and
In Biophys. J. Volume 88, 1970–1977, Mar
, IF: 4.463.

Columba: an integrated database of proteins, structures, and annotations
, , , , , , and
In BMC Bioinformatics Volume 6, 81, Mar
, IF: 5.423.

Conservation of cis prolyl bonds in proteins during evolution
, , , and
In Proteins Volume 58, 589–595, Feb
, IF: 5.239.

2004

Structural features of transmembrane helices
, and
In FEBS Lett. Volume 559, 145–151, Feb
.

Comparison of 2D similarity and 3D superposition. Application to searching a conformational drug database
, , and
In J Chem Inf Comput Sci Volume 44, 1816–1822,
.

2003

Loops In Proteins (LIP)–a comprehensive loop database for homology modelling
, and
In Protein Eng. Volume 16, 979–985, Dec
, IF: 2.065.

Accelerating screening of 3D protein data with a graph theoretical approach
, , , , , , and
In Bioinformatics Volume 19, 2442–2447, Dec
, IF: 6.701.

Inhomogeneous molecular density: reference packing densities and distribution of cavities within proteins
, , and
In Bioinformatics Volume 19, 2112–2121, Nov
.

Inverse sequence similarity of proteins does not imply structural similarity
, , and
In FEBS Lett. Volume 545, 105–109, Jun
, IF: 3.609.

A comprehensive view on proteasomal sequences: implications for the evolution of the proteasome
, , , , , and
In J. Mol. Biol. Volume 326, 1437–1448, Mar
, IF: 5.239.

2002

The RTP site shared by the HIV-1 Tat protein and the 11S regulator subunit alpha is crucial for their effects on proteasome function including antigen processing
, , , , , , , and
In J. Mol. Biol. Volume 323, 771–782, Nov
.

2001

Matching organic libraries with protein-substructures
, , , , and
In J. Comput. Aided Mol. Des. Volume 15, 811–817, Sep
, IF: 3.194.

2000

Conservation of substructures in proteins: interfaces of secondary structural elements in proteasomal subunits
, , , and
In J. Mol. Biol. Volume 299, 1147–1154, Jun
.

1999

Spare parts for helix-helix interaction
, and
In Protein Eng. Volume 12, 825–832, Oct
, IF: 3.209.

Homonyms and synonyms in the Dictionary of Interfaces in Proteins (DIP)
, and
In Bioinformatics Volume 15, 832–836, Oct
, IF: 6.701.

Sequence information within proteasomal prosequences mediates efficient integration of beta-subunits into the 20 S proteasome complex
, , , , and
In J. Mol. Biol. Volume 288, 117–128, Apr
, IF: 5.239.

1998

Dictionary of interfaces in proteins (DIP). Data bank of complementary molecular surface patches
, and
In J. Mol. Biol. Volume 280, 535–550, Jul
, IF: 6.701.

1997

Inverse sequence similarity in proteins and its relation to the three-dimensional fold
, , and
In FEBS Lett. Volume 414, 425–429, Sep
.

1991

On alpha-helices terminated by glycine. 2. Recognition by sequence patterns
and
In Biochem. Biophys. Res. Commun. Volume 180, 666–672, Oct
, IF: 2.836.

On alpha-helices terminated by glycine. 1. Identification of common structural features
and
In Biochem. Biophys. Res. Commun. Volume 180, 660–665, Oct
.

Occurrence of bifurcated three-center hydrogen bonds in proteins
, and
In FEBS Lett. Volume 288, 192–196, Aug
, IF: 3.609.

1990

Prediction of prolyl residues in cis-conformation in protein structures on the basis of the amino acid sequence
and
In FEBS Lett. Volume 277, 159–163, Dec
, IF: 3.609.