Insight on the mechanism of hexameric Pseudin-4 against bacterial membrane-mimetic environment A. S. VinuthaR. Rajasekaran OriginalPaper 27 June 2023 Pages: 419 - 434
Faster and more diverse de novo molecular optimization with double-loop reinforcement learning using augmented SMILES Esben Jannik BjerrumChristian MargreitterRaquel López-Ríos de Castro OriginalPaper 17 June 2023 Pages: 373 - 394
On the construction of LIECE models for the serotonin receptor 5-HT\(_{\text {2A}}\)R Aida ShahrakiJana SelentPeter Kolb OriginalPaper Open access 14 June 2023 Pages: 313 - 323
Integrated data-driven and experimental approaches to accelerate lead optimization targeting SARS-CoV-2 main protease Rohith Anand VarikotiKatherine J. SchultzNeeraj Kumar OriginalPaper 14 June 2023 Pages: 339 - 355
OFraMP: a fragment-based tool to facilitate the parametrization of large molecules Martin StroetBertrand CaronGunnar W. Klau OriginalPaper Open access 13 June 2023 Pages: 357 - 371
Molecular dynamics simulations reveal the inhibition mechanism of Cdc42 by RhoGDI1 Yijing ZhangShiyao ChenYaxue Zhao Correspondence 07 June 2023 Pages: 301 - 312
Elucidating the potential effects of point mutations on FGFR3 inhibitor resistance via combined molecular dynamics simulation and community network analysis Bo LiuJuntao DingWulan Li OriginalPaper 03 June 2023 Pages: 325 - 338
Insights into the coordination chemistry of antineoplastic doxorubicin with 3d-transition metal ions Zn2+, Cu2+, and VO2+: a study using well-calibrated thermodynamic cycles and chemical interaction quantum chemistry models Julieta Reyna-LunaLuis Soriano-AguedaMarco Franco-Pérez Correspondence 28 May 2023 Pages: 279 - 299
Study of SQ109 analogs binding to mycobacterium MmpL3 transporter using MD simulations and alchemical relative binding free energy calculations Marianna StampolakiIoannis StylianakisAntonios Kolocouris OriginalPaper Open access 02 May 2023 Pages: 245 - 264
TargIDe: a machine-learning workflow for target identification of molecules with antibiofilm activity against Pseudomonas aeruginosa João CarneiroRita P. MagalhãesSérgio F. Sousa OriginalPaper Open access 22 April 2023 Pages: 265 - 278
Computational insights into ligand–induced G protein and β-arrestin signaling of the dopamine D1 receptor Haoxi LiNikhil M. UrsNicole Horenstein OriginalPaper 15 April 2023 Pages: 227 - 244
Efficient screening of protein-ligand complexes in lipid bilayers using LoCoMock score Rikuri MoritaYasuteru ShigetaRyuhei Harada OriginalPaper 21 March 2023 Pages: 217 - 225
Improvement of multi-task learning by data enrichment: application for drug discovery Ekaterina A. SosninaSergey SosninMaxim V. Fedorov OriginalPaper 21 March 2023 Pages: 183 - 200
MM/GBSA prediction of relative binding affinities of carbonic anhydrase inhibitors: effect of atomic charges and comparison with Autodock4Zn Mackenzie TaylorJunming Ho OriginalPaper Open access 17 March 2023 Pages: 167 - 182
Structural mechanism of Fab domain dissociation as a measure of interface stability Nancy D. PomariciFranz WaiblKlaus R. Liedl OriginalPaper Open access 15 March 2023 Pages: 201 - 215
Inhibition mechanism of MRTX1133 on KRASG12D: a molecular dynamics simulation and Markov state model study Fanglin LiangZhengzhong KangJianxin Cheng OriginalPaper 28 February 2023 Pages: 157 - 166
GPCRLigNet: rapid screening for GPCR active ligands using machine learning Jacob M RemingtonKyle T McKayJianing Li OriginalPaper 25 February 2023 Pages: 147 - 156
pH-dependent solubility prediction for optimized drug absorption and compound uptake by plants Anne BoninFloriane MontanariAndreas H. Göller OriginalPaper 17 February 2023 Pages: 129 - 145
Identification of potential inhibitors of Mycobacterium tuberculosis shikimate kinase: molecular docking, in silico toxicity and in vitro experiments Talita Freitas de FreitasCandida Deves RothLuis Fernando Saraiva Macedo Timmers OriginalPaper 22 December 2022 Pages: 117 - 128
A combined ligand and target-based virtual screening strategy to repurpose drugs as putrescine uptake inhibitors with trypanocidal activity Manuel A. LlanosLucas N. AlbercaAlan Talevi OriginalPaper 10 December 2022 Pages: 75 - 90
The slow but steady rise of binding free energy calculations in drug discovery Huafeng Xu Review 05 December 2022 Pages: 67 - 74
DeepCubist: Molecular Generator for Designing Peptidomimetics based on Complex three-dimensional scaffolds Kohei UmederaAtsushi YoshimoriJürgen Bajorath OriginalPaper Open access 03 December 2022 Pages: 107 - 115
Computational investigation of functional water molecules in GPCRs bound to G protein or arrestin Jiaqi HuXianqiang SunJianxin Cheng OriginalPaper 02 December 2022 Pages: 91 - 105
Evaluation of interactions between the hepatitis C virus NS3/4A and sulfonamidobenzamide based molecules using molecular docking, molecular dynamics simulations and binding free energy calculations Jinhong RenTasneem M. VaidMichael E. Johnson Research 25 November 2022 Pages: 53 - 65
Molecular and thermodynamic insights into interfacial interactions between collagen and cellulose investigated by molecular dynamics simulation and umbrella sampling Huaiqin MaQingwen ShiLulu Ning OriginalPaper 25 November 2022 Pages: 39 - 51
Galileo: Three-dimensional searching in large combinatorial fragment spaces on the example of pharmacophores Christian MeyenburgUschi DolfusMatthias Rarey OriginalPaper Open access 24 November 2022 Pages: 1 - 16
Examining unsupervised ensemble learning using spectroscopy data of organic compounds Kedan HeDjenerly G. Massena OriginalPaper 21 November 2022 Pages: 17 - 37
Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constant Xiao LiuLei ZhengZhaoxi Sun OriginalPaper 17 November 2022 Pages: 879 - 894
Reliable gas-phase tautomer equilibria of drug-like molecule scaffolds and the issue of continuum solvation Andreas H. Göller OriginalPaper 02 November 2022 Pages: 805 - 824
The FMO2 analysis of the ligand-receptor binding energy: the Biscarbene-Gold(I)/DNA G-Quadruplex case study Roberto PaciottiCecilia ColettiNazzareno Re OriginalPaper 01 November 2022 Pages: 851 - 866
From oncoproteins to spike proteins: the evaluation of intramolecular stability using hydropathic force field Federica AgostaGlen E. KelloggPietro Cozzini OriginalPaper Open access 31 October 2022 Pages: 797 - 804
Physicochemical QSAR analysis of hERG inhibition revisited: towards a quantitative potency prediction Kiril LanevskijRemigijus DidziapetrisAndrius Sazonovas OriginalPaper 28 October 2022 Pages: 837 - 849
Improved prediction and characterization of blood-brain barrier penetrating peptides using estimated propensity scores of dipeptides Phasit CharoenkwanPramote ChumnanpuenWatshara Shoombuatong OriginalPaper 26 October 2022 Pages: 781 - 796
Enabling data-limited chemical bioactivity predictions through deep neural network transfer learning Ruifeng LiuSrinivas LaxminarayanAnders Wallqvist OriginalPaper 22 October 2022 Pages: 867 - 878
Protocol for iterative optimization of modified peptides bound to protein targets Rodrigo OchoaPilar CossioThomas Fox OriginalPaper Open access 19 October 2022 Pages: 825 - 835
An overview of the SAMPL8 host–guest binding challenge Martin AmezcuaJeffry SetiadiDavid L. Mobley OriginalPaper Open access 14 October 2022 Pages: 707 - 734
Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo Yunhui GeOliver J. MellingDavid L. Mobley OriginalPaper 06 October 2022 Pages: 767 - 779
A high quality, industrial data set for binding affinity prediction: performance comparison in different early drug discovery scenarios Andreas TosstorffMarkus G. RudolphBernd Kuhn OriginalPaper 25 September 2022 Pages: 753 - 765
Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: I. Standard procedure Xiao LiuLei ZhengZhaoxi Sun Research 22 September 2022 Pages: 735 - 752
Predicting octanol/water partition coefficients and pKa for the SAMPL7 challenge using the SM12, SM8 and SMD solvation models Sergio A. RodriguezJasmine Vy TranAndrew S. Paluch OriginalPaper 19 September 2022 Pages: 687 - 705
Epilogue to the Gerald Maggiora Festschrift: a tribute to an exemplary mentor, colleague, collaborator, and innovator Veerabahu ShanmugasundaramJürgen BajorathLinda L. Restifo Correspondence 17 September 2022 Pages: 623 - 638
Prot2Prot: a deep learning model for rapid, photorealistic macromolecular visualization Jacob D. Durrant OriginalPaper Open access 26 August 2022 Pages: 677 - 686
FastGrow: on-the-fly growing and its application to DYRK1A Patrick PennerVirginie MartinyMatthias Rarey OriginalPaper Open access 22 August 2022 Pages: 639 - 651
Covalent docking in CDOCKER Yujin WuCharles L. Brooks III Correspondence 19 August 2022 Pages: 563 - 574
Unveiling the G4-PAMAM capacity to bind and protect Ang-(1-7) bioactive peptide by molecular dynamics simulations L. América ChiSomayeh AsgharpourMarlet Martínez-Archundia OriginalPaper 08 August 2022 Pages: 653 - 675
Des3PI: a fragment-based approach to design cyclic peptides targeting protein–protein interactions Maxence DelaunayTâp Ha-Duong OriginalPaper 06 August 2022 Pages: 605 - 621
Modeling receptor flexibility in the structure-based design of KRASG12C inhibitors Kai ZhuCui LiBrian Lanman OriginalPaper Open access 05 August 2022 Pages: 591 - 604
Crystal polymorphism and spectroscopical properties of sulfonamides in solid state by means of First Principles calculations C. Ignacio Sainz-DíazAlexander Pérez de la LuzCatalina Soriano-Correa OriginalPaper Open access 26 July 2022 Pages: 549 - 562
Insight into the mechanism of molecular recognition between human Integrin-Linked Kinase and Cpd22 and its implication at atomic level Javier García-MarínDiego Rodríguez-PuyolJuan J. Vaquero OriginalPaper Open access 23 July 2022 Pages: 575 - 589
On the force field optimisation of \(\beta\)-lactam cores using the force field Toolkit Qiyang WuTianyang HuangYing-Chih Chiang OriginalPaper Open access 11 July 2022 Pages: 537 - 547