News: Algorithmisches Molekulares Design14. Juni 2024|AMD NewsNew Paper: Database-Driven Identification of Structurally Similar Protein-Protein InterfacesFoto: Christiane EhrtExamining the similarity between interfaces of protein-protein complexes can provide valuable insights into protein functions and assist in drug...30. Mai 2024|AMD NewsNew Paper: SiteMine: Large-scale binding site similarity searching in protein structure databasesFoto: Thorben ReimDrug discovery and design pose various challenges such as drug repurposing, analysis of protein-ligand and protein-protein complexes, ligand...20. Dezember 2023|AMD NewsNew Paper: Redocking the PDBFoto: Florian FlachsenbergRedocking the PDB - How to get an honest estimate on docking success rate? Docking tools are usually evaluated on relatively small subselections of...7. November 2023|AMD NewsNew Paper: Full Modification Control over Retrosynthetic Routes for Guided Optimization of Lead StructuresFoto: Uschi DolfusSynthesizability is essential for compounds designed in silico. Regardless, synthetic accessibility is often considered only as an afterthought in the...6. November 2023|AMD NewsNew Paper: Searching similar local 3D micro-environments in protein structure databases with MicroMinerFoto: Jochen SiegInterested in the structural change induced by single mutations? MicroMiner is a new tool that provides large-scale data on the structural details of...31. August 2023|AMD NewsNew Paper: LifeSoaks: a tool for analyzing solvent channels in protein crystals and obstacles for soaking experimentsFoto: Jonathan Pletzer-ZelgertDue to the geometric complexity of protein structures, solvent-filled channels and cavities are omnipresent in their crystal arrangements. These...8. Juni 2023|AMD NewsReview: Navigating large chemical spaces in early-phase drug discoveryFoto: Malte KornThe use of chemical spaces for drug discovery has become a major focus in the scientific community, highlighting their growing importance. This review...5. Mai 2023|AMD NewsNew Paper: Binding Site Detection Remastered: Enabling Fast, Robust, and Reliable Binding Site Detection and Descriptor Calculation with DoGSite3Foto: Joel GraefDetecting binding sites in protein and nucleic acid structures is a crucial starting point for structure-based investigations for enzyme function...11. April 2023|AMD NewsNew Paper: Modeling with Alternate Locations in X-ray Protein StructureFoto: Toben GutermuthCrystallographic protein structures sometimes contain multiple conformations of side chains, ligands or even larger protein parts like flexible loops...22. Dezember 2022|AMD NewsNew Paper: Galileo: Three-dimensional searching in large combinatorial fragment spaces on the example of pharmacophoresFoto: Christian MeyenburgChemical fragment spaces contain billions of molecules. This makes the process of searching them for bioactive compounds computationally challenging...30. Oktober 2022|AMD NewsNew Paper: Small molecule superposition: A comprehensive overview on pose scoring of the latest methodsFoto: Sophia HönigThe superposition of small molecules is still one of the main pillars of ligand-based drug discovery. It is a standard technique in molecular modeling...19. Oktober 2022|AMD NewsGCB 2023 in HamburgFoto: GCBWir freuen uns, Ihnen mitteilen zu können, dass die DECHEMA und die Universität Hamburg die German Conference on Bioinformatics (GCB) 2023 auf dem...30. September 2022|AMD NewsNew Paper: Visualizing Generic Reaction PatternsFoto: Uschi DolfusComputer-readable generic reaction schemes are a fundamental technique in the in silico drug design process. Due to their complexity and the richness...23. August 2022|AMD NewsNew Paper: AMD group presents FastGrowFoto: Patrick PennerTogether with our colaboration partners Servier and BioSolveIT we are happy to present FastGrow, an index-based rapid fragment growing for...27. Juli 2022|AMD NewsNew Paper: Synthesis-Aware Generation of Structural AnaloguesFoto: Uschi DolfusSynthesizability is still one of the main obstacles of drug candidates designed in silico. Computer-aided synthesis planning methods try to tackle...29. Juni 2022|AMD NewsProf. Rarey im Interview mit ACS c&en über Chemical Space TechnologieDie Juni-Ausgabe des News-Journals c&en der Amerikanischen Chemischen Gesellschaft (ACS) berichtet über die Navigation im chemischen Raum für die...3. Juni 2022|AMD NewsNew Paper: Calculating and Optimizing Physicochemical Property Distributions of Large Combinatorial Fragment SpacesFoto: Louis BellmannLarge collections of compounds are nowadays given in a combinatorial fashion since they are too large to be presented in an enumerated way...18. Mai 2022|AMD NewsDrei Awards für AG Rarey auf der GCCFoto: Stefan GüssregenDrei Mitglieder der Arbeitsgruppe Algorithmisches und Molekulares Design (AMD) von Prof. Dr. Matthias Rarey wurden auf der 17. Deutschen Tagung für...4. Mai 2022|AMD NewsNew Paper: ProteinsPlus: a comprehensive collection of web-based molecular modeling toolsFoto: Katrin Schöning-StierandThe ProteinsPlus (https://proteins.plus) web service is a steadily growing and developing collection of ready-to-use online tools for structure-based...8. April 2022|AMD NewsNew Paper: Predicting structural features of proteins from deep-sea organismsPredicting molecular protein adaptations is a key challenge in protein engineering. In our recent publication we analyze adaptations of protein...Zum Archiv