User-centric design of a 3D search interface for protein-ligand complexes Konrad DiedrichChristiane EhrtMatthias Rarey OriginalPaper Open access 30 May 2024 Article: 23
Correlation of protein binding pocket properties with hits’ chemistries used in generation of ultra-large virtual libraries Robert X. SongMarc C. NicklausNadya I. Tarasova OriginalPaper Open access 16 May 2024 Article: 22
Reactivities of acrylamide warheads toward cysteine targets: a QM/ML approach to covalent inhibitor design Aaron D. DanilackCallum J. DicksonJose S. Duca OriginalPaper 01 May 2024 Article: 21
De novo drug design as GPT language modeling: large chemistry models with supervised and reinforcement learning Gavin Ye OriginalPaper Open access 22 April 2024 Article: 20
From UK-2A to florylpicoxamid: Active learning to identify a mimic of a macrocyclic natural product Ann E. ClevesAjay N. JainErin N. Hancock OriginalPaper Open access 17 April 2024 Article: 19
On the relevance of query definition in the performance of 3D ligand-based virtual screening Javier VázquezRicardo GarcíaEnric Herrero OriginalPaper Open access 04 April 2024 Article: 18
Computational peptide discovery with a genetic programming approach Nicolas ScalzittiIliya MiralavyWolfgang Banzhaf OriginalPaper Open access 03 April 2024 Article: 17
Identifying and characterising promising small molecule inhibitors of kinesin spindle protein using ligand-based virtual screening, molecular docking, molecular dynamics and MM‑GBSA calculations Samia A. Elseginy OriginalPaper Open access 01 April 2024 Article: 16
Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 Mpro Irem N. ZenginM. Serdar KocaAbdulkadir Kocak OriginalPaper Open access 27 March 2024 Article: 15
The AI-driven Drug Design (AIDD) platform: an interactive multi-parameter optimization system integrating molecular evolution with physiologically based pharmacokinetic simulations Jeremy JonesRobert D. ClarkMarvin Waldman OriginalPaper 19 March 2024 Article: 14
SpaceGrow: efficient shape-based virtual screening of billion-sized combinatorial fragment spaces Sophia M. N. HönigFlorian FlachsenbergMatthias Rarey OriginalPaper Open access 17 March 2024 Article: 13
Correction: Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design Ajay N. JainAlexander C. BruecknerLuciano Mueller Correction Open access 13 March 2024 Article: 12
Molecular dynamics simulations as a guide for modulating small molecule aggregation Azam NesabiJas KalayanRichard A. Bryce OriginalPaper Open access 12 March 2024 Article: 11
Molecule auto-correction to facilitate molecular design Alan KerstjensHans De Winter OriginalPaper Open access 16 February 2024 Article: 10
Rethinking the applicability domain analysis in QSAR models Jose R. MoraEdgar A. MarquezStephen J. Barigye OriginalPaper 14 February 2024 Article: 9
Deciphering the molecular choreography of Janus kinase 2 inhibition via Gaussian accelerated molecular dynamics simulations: a dynamic odyssey Md Fulbabu SkSunanda SamantaParimal Kar OriginalPaper 07 February 2024 Article: 8
A deep neural network: mechanistic hybrid model to predict pharmacokinetics in rat Florian FührerAndrea GruberSebastian Schneckener OriginalPaper 31 January 2024 Article: 7
Identification of a druggable site on GRP78 at the GRP78-SARS-CoV-2 interface and virtual screening of compounds to disrupt that interface Maria LazouJonathan R. HuttonDiane Joseph-McCarthy OriginalPaper 24 January 2024 Article: 6
Molecular dynamics study on micelle-small molecule interactions: developing a strategy for an extensive comparison Aleksei KabedevChristel A. S. BergströmPer Larsson OriginalPaper Open access 16 December 2023 Article: 5
QM assisted ML for 19F NMR chemical shift prediction Patrick PennerAnna Vulpetti OriginalPaper 12 December 2023 Article: 4
Open-ComBind: harnessing unlabeled data for improved binding pose prediction Andrew T. McNuttDavid Ryan Koes OriginalPaper Open access 08 December 2023 Article: 3
Correction: Exploring DrugCentral: from molecular structures to clinical effects Liliana HalipSorin AvramTudor I. Oprea Correction Open access 02 December 2023 Article: 2
Binding of small molecule inhibitors to RNA polymerase-Spt5 complex impacts RNA and DNA stability Adan GallardoBercem Dutagaci OriginalPaper Open access 21 November 2023 Article: 1
Predicting absolute aqueous solubility by applying a machine learning model for an artificially liquid-state as proxy for the solid-state Sadra Kashef Ol GhetaAnne BoninAndreas H. Göller OriginalPaper 25 October 2023 Pages: 765 - 789
Correction to: Computational workflow for discovering small molecular binders for shallow binding sites by integrating molecular dynamics simulation, pharmacophore modeling, and machine learning: STAT3 as case study Nour Jamal JaradatMamon HatmalMutasem Omar Taha Correction 19 October 2023 Pages: 679 - 679
Artificial intelligence for prediction of biological activities and generation of molecular hits using stereochemical information Tiago O. PereiraMaryam AbbasiJoel P. Arrais OriginalPaper Open access 17 October 2023 Pages: 791 - 806
MASSA Algorithm: an automated rational sampling of training and test subsets for QSAR modeling Gabriel Corrêa VeríssimoSimone Queiroz PantaleãoVinícius Gonçalves Maltarollo OriginalPaper 07 October 2023 Pages: 735 - 754
The in silico identification of novel broad-spectrum antidotes for poisoning by organophosphate anticholinesterases Sohaib HabiballahJanice ChambersBrad Reisfeld OriginalPaper 05 October 2023 Pages: 755 - 764
Mur ligase F as a new target for the flavonoids quercitrin, myricetin, and (–)-epicatechin Martina Hrast RambaherIrena ZdovcRok Frlan OriginalPaper Open access 05 October 2023 Pages: 721 - 733
Cooperative and structural relationships of the trimeric Spike with infectivity and antibody escape of the strains Delta (B.1.617.2) and Omicron (BA.2, BA.5, and BQ.1) Anacleto Silva de SouzaRobson Francisco de SouzaCristiane Rodrigues Guzzo PERSPECTIVE 04 October 2023 Pages: 585 - 606
TeM-DTBA: time-efficient drug target binding affinity prediction using multiple modalities with Lasso feature selection Tanya LiyaqatTanvir AhmadChandni Saxena PERSPECTIVE 30 September 2023 Pages: 573 - 584
Correction to: Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory Ioannis StylianakisNikolaos ZervosAntonios Kolocouris Correction Open access 29 September 2023 Pages: 657 - 657
Improving the accuracy of the FMO binding affinity prediction of ligand-receptor complexes containing metals R. PaciottiA. MarroneN. Re OriginalPaper Open access 25 September 2023 Pages: 707 - 719
Exploring DrugCentral: from molecular structures to clinical effects Liliana HalipSorin AvramTudor I. Oprea ReviewPaper Open access 14 September 2023 Pages: 681 - 694
Discovery of novel and potent InhA direct inhibitors by ensemble docking-based virtual screening and biological assays Qianqian ZhangJianting HanHuanxiang Liu OriginalPaper 29 August 2023 Pages: 695 - 706
ChemFlow_py: a flexible toolkit for docking and rescoring Luca MonariKatia GalentinoMarco Cecchini OriginalPaper 24 August 2023 Pages: 565 - 572
Computational workflow for discovering small molecular binders for shallow binding sites by integrating molecular dynamics simulation, pharmacophore modeling, and machine learning: STAT3 as case study Nour Jamal JaradatMamon HatmalMutasem Omar Taha OriginalPaper 19 August 2023 Pages: 659 - 678
Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory Ioannis StylianakisNikolaos ZervosAntonios Kolocouris OriginalPaper Open access 19 August 2023 Pages: 607 - 656
A least-squares-fitting procedure for an efficient preclinical ranking of passive transport across the blood–brain barrier endothelium Christian JorgensenEvan P. TroendleMartin B. Ulmschneider OriginalPaper Open access 12 August 2023 Pages: 537 - 549
Improving drug discovery with a hybrid deep generative model using reinforcement learning trained on a Bayesian docking approximation Youjin XiongYiqing WangChristopher J. Butch OriginalPaper 08 August 2023 Pages: 507 - 517
Investigating the role of glycans in Omicron sub-lineages XBB.1.5 and XBB.1.16 binding to host receptor using molecular dynamics and binding free energy calculations Jaikee Kumar SinghJai SinghSandeep Kumar Srivastava OriginalPaper 05 August 2023 Pages: 551 - 563
Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design Ajay N. JainAlexander C. BruecknerLuciano Mueller Articles Open access 03 August 2023 Pages: 519 - 535
PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams Konrad DiedrichBennet KrauseMatthias Rarey OriginalPaper Open access 29 July 2023 Pages: 491 - 503
Exploring binding positions and backbone conformations of peptide ligands of proteins with a backbone-centred statistical energy function Lu ZhangHaiyan Liu OriginalPaper 27 July 2023 Pages: 463 - 478
Enhancement by pyrazolones of colistin efficacy against mcr-1-expressing E. coli: an in silico and in vitro investigation Chonnikan HanpaiboolPuey OunjaiThanyada Rungrotmongkol OriginalPaper 24 July 2023 Pages: 479 - 489
Correction to: Assessing the performance of docking, FEP, and MM/GBSA methods on a series of KLK6 inhibitors Wemenes José Lima SilvaRenato Ferreira de Freitas Correction 22 July 2023 Pages: 505 - 505
Polygalic acid inhibits african swine fever virus polymerase activity: findings from machine learning and in vitro testing Jiwon ChoiHyundo LeeSoon B. Hwang Original Research 15 July 2023 Pages: 453 - 461
ADis-QSAR: a machine learning model based on biological activity differences of compounds Gyoung Jin ParkNam Sook Kang OriginalPaper 29 June 2023 Pages: 435 - 451
Assessing the performance of docking, FEP, and MM/GBSA methods on a series of KLK6 inhibitors Wemenes José Lima SilvaRenato Ferreira de Freitas OriginalPaper 28 June 2023 Pages: 407 - 418
COSMO-RS blind prediction of distribution coefficients and aqueous pKa values from the SAMPL8 challenge Michael DiedenhofenFrank EckertSelman Terzi OriginalPaper 27 June 2023 Pages: 395 - 405
