Journal of computer-aided molecular design

Keyphrases

Publications

volume 38, number 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. Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 38 (1) (2024)
Jose R Mora, Edgar A Marquez, Noel Pérez-Pérez, Ernesto Contreras-Torres, Yunierkis Perez-Castillo, Guillermin Agüero-Chapin, Felix Martinez-Rios, Yovani Marrero-Ponce, Stephen J Barigye
Rethinking the applicability domain analysis in QSAR models. Journal of computer-aided molecular design 38 (1) (2024)
Irem N Zengin, M Serdar Koca, Omer Tayfuroglu, Muslum Yildiz, Abdulkadir Kocak
Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 M pro . Journal of computer-aided molecular design 38 (1) (2024)
Javier Vázquez, Ricardo García, Paula Llinares, Francisco Javier Luque, Enric Herrero
On the relevance of query definition in the performance of 3D ligand-based virtual screening. Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 38 (1) (2024)
Alan Kerstjens, Hans De Winter
Molecule auto-correction to facilitate molecular design. Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 38 (1) (2024)
Javier Vázquez, Ricardo García, Paula Llinares, Francisco Javier Luque, Enric Herrero
On the relevance of query definition in the performance of 3D ligand-based virtual screening. Journal of computer-aided molecular design 38 (1) (2024)
Irem N Zengin, M Serdar Koca, Omer Tayfuroglu, Muslum Yildiz, Abdulkadir Kocak
Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 M pro . Journal of computer-aided molecular design 38 (1) (2024)
Alan Kerstjens, Hans De Winter
Molecule auto-correction to facilitate molecular design. Journal of computer-aided molecular design 38 (1) (2024)
Jeremy O 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. Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 38 (1) (2024)
Alan Kerstjens, Hans De Winter
Molecule auto-correction to facilitate molecular design. Journal of computer-aided molecular design 38 (1) (2024)
Jose R Mora, Edgar A Marquez, Noel Pérez-Pérez, Ernesto Contreras-Torres, Yunierkis Perez-Castillo, Guillermin Agüero-Chapin, Felix Martinez-Rios, Yovani Marrero-Ponce, Stephen J Barigye
Rethinking the applicability domain analysis in QSAR models. Journal of computer-aided molecular design 38 (1) (2024)
Gavin Ye
De novo drug design as GPT language modeling: large chemistry models with supervised and reinforcement learning. Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 38 (1) (2024)
Gavin Ye
De novo drug design as GPT language modeling: large chemistry models with supervised and reinforcement learning. Journal of computer-aided molecular design 38 (1) (2024)
Gavin Ye
De novo drug design as GPT language modeling: large chemistry models with supervised and reinforcement learning. Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 38 (1) (2024)
Javier Vázquez, Ricardo García, Paula Llinares, Francisco Javier Luque, Enric Herrero
On the relevance of query definition in the performance of 3D ligand-based virtual screening. Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 38 (1) (2024)
Irem N Zengin, M Serdar Koca, Omer Tayfuroglu, Muslum Yildiz, Abdulkadir Kocak
Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 M pro . Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 38 (1) (2024)
Jeremy O 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. Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 38 (1) (2024)
Javier Vázquez, Ricardo García, Paula Llinares, Francisco Javier Luque, Enric Herrero
On the relevance of query definition in the performance of 3D ligand-based virtual screening. Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 38 (1) (2024)
Alan Kerstjens, Hans De Winter
Molecule auto-correction to facilitate molecular design. Journal of computer-aided molecular design 38 (1) (2024)
Gavin Ye
De novo drug design as GPT language modeling: large chemistry models with supervised and reinforcement learning. Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 38 (1) (2024)
Gavin Ye
De novo drug design as GPT language modeling: large chemistry models with supervised and reinforcement learning. Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 38 (1) (2024)
Aaron D Danilack, Callum J Dickson, Cihan Soylu, Mike Fortunato, Stephane Rodde, Hagen Munkler, Viktor Hornak, Jose S Duca
Reactivities of acrylamide warheads toward cysteine targets: a QM/ML approach to covalent inhibitor design. Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 38 (1) (2024)