News: Algorithmisches Molekulares Design15 November 2024|AMD NewsTwo awards for the Rarey group at the GCC 2024Photo: Emanuel EhmkiWe are honored to share that our work on chemical fragment spaces received two awards of the Gesellschaft Deutscher Chemiker e.V. at the GCC: Louis...14 June 2024|AMD NewsNew Paper: Database-Driven Identification of Structurally Similar Protein-Protein InterfacesPhoto: Christiane EhrtExamining the similarity between interfaces of protein-protein complexes can provide valuable insights into protein functions and assist in drug...30 May 2024|AMD NewsNew Paper: SiteMine: Large-scale binding site similarity searching in protein structure databasesPhoto: Thorben ReimDrug discovery and design pose various challenges such as drug repurposing, analysis of protein-ligand and protein-protein complexes, ligand...20 December 2023|AMD NewsNew Paper: Redocking the PDBPhoto: 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 StructuresPhoto: 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 MicroMinerPhoto: 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 experimentsPhoto: Jonathan Pletzer-ZelgertDue to the geometric complexity of protein structures, solvent-filled channels and cavities are omnipresent in their crystal arrangements. These...8 June 2023|AMD NewsReview: Navigating large chemical spaces in early-phase drug discoveryPhoto: 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 May 2023|AMD NewsNew Paper: Binding Site Detection Remastered: Enabling Fast, Robust, and Reliable Binding Site Detection and Descriptor Calculation with DoGSite3Photo: 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 StructurePhoto: Toben GutermuthCrystallographic protein structures sometimes contain multiple conformations of side chains, ligands or even larger protein parts like flexible loops...22 December 2022|AMD NewsNew Paper: Galileo: Three-dimensional searching in large combinatorial fragment spaces on the example of pharmacophoresPhoto: Christian MeyenburgChemical fragment spaces contain billions of molecules. This makes the process of searching them for bioactive compounds computationally challenging...30 October 2022|AMD NewsNew Paper: Small molecule superposition: A comprehensive overview on pose scoring of the latest methodsPhoto: 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 October 2022|AMD NewsGCB 2023 in HamburgPhoto: GCBWe are pleased to announce that DECHEMA and Universität Hamburg will host the German Conference on Bioinformatics (GCB) 2023 on the DESY Campus in...30 September 2022|AMD NewsNew Paper: Visualizing Generic Reaction PatternsPhoto: 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 FastGrowTogether with our colaboration partners Servier and BioSolveIT we are happy to present FastGrow, an index-based rapid fragment growing for...27 July 2022|AMD NewsNew Paper: Synthesis-Aware Generation of Structural AnaloguesPhoto: Uschi DolfusSynthesizability is still one of the main obstacles of drug candidates designed in silico. Computer-aided synthesis planning methods try to tackle...29 June 2022|AMD NewsProf. Rarey interviewed by ACS c&en about chemical space technologyThe June issue of the News-Journal c&en of the American Chemical Society (ACS) reports on navigating chemical space for the development of new drugs...3 June 2022|AMD NewsNew Paper: Calculating and Optimizing Physicochemical Property Distributions of Large Combinatorial Fragment SpacesPhoto: 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 May 2022|AMD NewsThree awards for Research Group Rarey on the GCCPhoto: Stefan GüssregenThree members of the Algorithmic and Molecular Design (AMD) group lead by Prof. Dr. Matthias Rarey have won awards at the 17th German Conference on...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...Show all news