J. Comput. Aided Mol. Des.

Keyphrases

Publications

volume 38, number 1, 2024

Adan Gallardo, Bercem Dutagaci
Binding of small molecule inhibitors to RNA polymerase-Spt5 complex impacts RNA and DNA stability. J. Comput. Aided Mol. Des. 38 (1) (2024)
Patrick Penner, Anna Vulpetti
F NMR chemical shift prediction. J. Comput. Aided Mol. Des. 38 (1) (2024)
Daniel K. Gehlhaar, Daniel J. Mermelstein
FitScore: a fast machine learning-based score for 3D virtual screening enrichment. J. Comput. Aided Mol. Des. 38 (1) (2024)
Robert X. Song, Marc C. Nicklaus, Nadya I. Tarasova
Correlation of protein binding pocket properties with hits' chemistries used in generation of ultra-large virtual libraries. J. Comput. Aided Mol. Des. 38 (1) (2024)
Aleksei Kabedev, Christel A. S. Bergström, Per Larsson
Molecular dynamics study on micelle-small molecule interactions: developing a strategy for an extensive comparison. J. Comput. Aided Mol. Des. 38 (1) (2024)
Javier Vázquez, Ricardo García, Paula Llinares, F. Javier Luque, Enric Herrero
On the relevance of query definition in the performance of 3D ligand-based virtual screening. J. Comput. Aided Mol. Des. 38 (1) (2024)
Ajay N. Jain, Alexander C. Brueckner, Christine Jorge, Ann E. Cleves, Purnima Khandelwal, Janet Caceres Cortes, Luciano Mueller
Correction: Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design. J. Comput. Aided Mol. Des. 38 (1) (2024)
Samia A. Elseginy
Identifying and characterising promising small molecule inhibitors of kinesin spindle protein using ligand-based virtual screening, molecular docking, molecular dynamics and MM‑GBSA calculations. J. Comput. Aided Mol. Des. 38 (1) (2024)
Andrew T. McNutt, David Ryan Koes
Open-ComBind: harnessing unlabeled data for improved binding pose prediction. J. Comput. Aided Mol. Des. 38 (1) (2024)
Alexander C. Brueckner, Benjamin Shields, Palani Kirubakaran, Alexander Suponya, Manoranjan Panda, Shana L. Posy, Stephen R. Johnson, Sirish Kaushik Lakkaraju
MDFit: automated molecular simulations workflow enables high throughput assessment of ligands-protein dynamics. J. Comput. Aided Mol. Des. 38 (1) (2024)
Konrad Diedrich, Christiane Ehrt, Joel Graef, Martin Poppinga, Norbert Ritter, Matthias Rarey
User-centric design of a 3D search interface for protein-ligand complexes. J. Comput. Aided Mol. Des. 38 (1) (2024)
José Ramón Mora, Edgar Márquez, Noel Pérez-Pérez, Ernesto Contreras-Torres, Yunierkis Pérez-Castillo, Guillermín Agüero-Chapín, Felix Martinez-Rios, Yovani Marrero-Ponce, Stephen J. Barigye
Rethinking the applicability domain analysis in QSAR models. J. Comput. Aided Mol. Des. 38 (1) (2024)
Florian Führer, Andrea Gruber, Holger Diedam, Andreas H. Göller, Stephan Menz, Sebastian Schneckener
A deep neural network: mechanistic hybrid model to predict pharmacokinetics in rat. J. Comput. Aided Mol. Des. 38 (1) (2024)
Irem N. Zengin, M. Serdar Koca, Omer Tayfuroglu, Muslum Yildiz, Abdulkadir Kocak
. J. Comput. Aided Mol. Des. 38 (1) (2024)
Daniel A. M. Pais, Jan-Peter A. Mayer, Karin Felderer, Maria B. Batalha, Timo Eichner, Sofia T. Santos, Raman Kumar, Sandra D. Silva, Hitto Kaufmann
Holistic in silico developability assessment of novel classes of small proteins using publicly available sequence-based predictors. J. Comput. Aided Mol. Des. 38 (1) (2024)
Wen-Chieh Huang, Chia-Hung Hsu, Titus V. Albu, Chia-Ning Yang
Structural impacts of two disease-linked ADAR1 mutants: a molecular dynamics study. J. Comput. Aided Mol. Des. 38 (1) (2024)
Yuanyuan Shu, Jianda Yue, Yaqi Li, Yekui Yin, Jiaxu Wang, Tingting Li, Xiao He, Songping Liang, Gaihua Zhang, Zhonghua Liu, Ying Wang
Development of human lactate dehydrogenase a inhibitors: high-throughput screening, molecular dynamics simulation and enzyme activity assay. J. Comput. Aided Mol. Des. 38 (1) (2024)
Azam Nesabi, Jas Kalayan, Sara Al Rawashdeh, Mohammad A. Ghattas, Richard A. Bryce
Molecular dynamics simulations as a guide for modulating small molecule aggregation. J. Comput. Aided Mol. Des. 38 (1) (2024)
Hyosoon Jang, Sangmin Seo, Sanghyun Park, Byung Ju Kim, Geon-Woo Choi, Jonghwan Choi, Chihyun Park
De novo drug design through gradient-based regularized search in information-theoretically controlled latent space. J. Comput. Aided Mol. Des. 38 (1) (2024)
Liliana Halip, Sorin I. Avram, Ramona Curpan, Ana Borota, Alina Bora, Cristian Bologa, Tudor I. Oprea
Correction: Exploring DrugCentral: from molecular structures to clinical effects. J. Comput. Aided Mol. Des. 38 (1) (2024)
Aaron D. Danilack, Callum J. Dickson, Cihan Soylu, Mike Fortunato, Stephane Rodde, Hagen Munkler, Viktor Hornak, José S. Duca
Reactivities of acrylamide warheads toward cysteine targets: a QM/ML approach to covalent inhibitor design. J. Comput. Aided Mol. Des. 38 (1) (2024)
Nicolas Scalzitti, Iliya Miralavy, David E. Korenchan, Christian T. Farrar, Assaf A. Gilad, Wolfgang Banzhaf
Computational peptide discovery with a genetic programming approach. J. Comput. Aided Mol. Des. 38 (1) (2024)
Ann E. Cleves, Ajay N. Jain, David A. Demeter, Zachary A. Buchan, Jeremy Wilmot, Erin N. Hancock
From UK-2A to florylpicoxamid: Active learning to identify a mimic of a macrocyclic natural product. J. Comput. Aided Mol. Des. 38 (1) (2024)
Gavin Ye
De novo drug design as GPT language modeling: large chemistry models with supervised and reinforcement learning. J. Comput. Aided Mol. Des. 38 (1) (2024)
Laura Guasch, Niels Maeder, John G. Cumming, Christian Kramer
From mundane to surprising nonadditivity: drivers and impact on ML models. J. Comput. Aided Mol. Des. 38 (1) (2024)
Sophia M. N. Hönig, Florian Flachsenberg, Christiane Ehrt, Alexander Neumann, Robert Schmidt, Christian Lemmen, Matthias Rarey
SpaceGrow: efficient shape-based virtual screening of billion-sized combinatorial fragment spaces. J. Comput. Aided Mol. Des. 38 (1) (2024)
Md Fulbabu Sk, Sunanda Samanta, Sayan Poddar, Parimal Kar
Deciphering the molecular choreography of Janus kinase 2 inhibition via Gaussian accelerated molecular dynamics simulations: a dynamic odyssey. J. Comput. Aided Mol. Des. 38 (1) (2024)
Kaipeng Li, Lijun Liu
-trap derived from TEAD4 helical hairpin to selectively capture YAP α1-helix with potent antitumor activity. J. Comput. Aided Mol. Des. 38 (1) (2024)
Lucas A. Garro, Matias F. Andrada, Esteban G. Vega-Hissi, Sonia Barberis, Juan C. Garro Martinez
Development of QSARs for cysteine-containing di- and tripeptides with antioxidant activity:influence of the cysteine position. J. Comput. Aided Mol. Des. 38 (1) (2024)
Jeremy Jones, Robert D. Clark, Michael S. Lawless, David W. Miller, Marvin Waldman
The AI-driven Drug Design (AIDD) platform: an interactive multi-parameter optimization system integrating molecular evolution with physiologically based pharmacokinetic simulations. J. Comput. Aided Mol. Des. 38 (1) (2024)
Alan Kerstjens, Hans De Winter
Molecule auto-correction to facilitate molecular design. J. Comput. Aided Mol. Des. 38 (1) (2024)
Maria Lazou, Jonathan R. Hutton, Arijit Chakravarty, Diane Joseph-McCarthy
Identification of a druggable site on GRP78 at the GRP78-SARS-CoV-2 interface and virtual screening of compounds to disrupt that interface. J. Comput. Aided Mol. Des. 38 (1) (2024)

volume 37, number 4, 2023

volume 37, number 5, 2023

volume 37, number 7, 2023

volume 37, number 8, 2023

volume 37, number 9, 2023