News14 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...22 February 2024|BM NewsNew Paper: Differentiable partition function calculation for RNAIf you are clever, you can optimise RNA sequences as if they were smooth, continuous objects. If you are even cleverer, you can optimise parameters as...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: 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 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 FastGrowPhoto: Patrick PennerTogether 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 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 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 NewsDrei Awards für AG Rarey auf der GCCPhoto: Stefan GüssregenDrei Mitglieder der Arbeitsgruppe Algorithmisches und Molekulares Design (AMD) von Prof. Dr. Matthias Rarey wurden auf der 17. Deutschen Tagung für...4 May 2022|AMD NewsNew Paper: ProteinsPlus: a comprehensive collection of web-based molecular modeling toolsPhoto: 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...Show all news
