News31 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...3 May 2022|ZBH NewsAnschub für Data Science in den NaturwissenschaftenPhoto: DESY/MayerDie Naturwissenschaften haben in den vergangenen Jahrzehnten mithilfe des Einsatzes von Computern große Fortschritte gemacht. Für die Entwicklung...Contribution from the news channel MIN8 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...6 April 2022|AMD NewsNew Paper: The Torsion Library - Semiautomated Improvement of Torsion Rules with SMARTScomparePhoto: Patrick PennerThe Torsion Library - Semiautomated Improvement of Torsion Rules with SMARTScompare Torsion angles are the most challenging part of any molecular...27 January 2022|AMD NewsNew Paper: Interpretation of Structure–Activity Relationships in Real-World Drug Design Data Sets Using Explainable Artificial IntelligenceNeural Networks have achieved high predictive performance in a variety of tasks related to Drug-Design. However their inherent black box character...21 January 2022|AMD NewsNew Paper: Comparison of Combinatorial Fragment Spaces and Its Application to Ultralarge Make-on-Demand Compound CatalogsPhoto: Louis BellmannComparison of Ultralage Make-on-demand compound catalogs for the first time Calculating the compound overlap of two or more chemical libraries is a...15 September 2021|AMD NewsNew Paper: Searching Geometric Patterns in Protein Binding Sites and Their Application to Data Mining in Protein Kinase StructuresPhoto: Figure: The human kinome trees in this figure were created with KinMap (http://www.kinhub.org/kinmap/)Protein kinase research encounters several challenges, the most serious one being the improvement of inhibitor selectivity through compound...Show all news
