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ORCIDJournal of Computer-Aided Molecular Design, Volume 36
Volume 36, Number 1, January 2022
- Daniel Markthaler, Hamzeh Kraus
, Niels Hansen:
Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange. 1-9 - Lorenzo Di Rienzo, Luca De Flaviis, Giancarlo Ruocco, Viola Folli, Edoardo Milanetti:
Binding site identification of G protein-coupled receptors through a 3D Zernike polynomials-based method: application to C. elegans olfactory receptors. 11-24 - Sergio R. Ribone, S. Alexis Paz, Cameron F. Abrams, Marcos Ariel Villarreal:
Target identification for repurposed drugs active against SARS-CoV-2 via high-throughput inverse docking. 25-37 - Lubabah A. Mousa, Mámon M. Hatmal, Mutasem O. Taha:
Exploiting activity cliffs for building pharmacophore models and comparison with other pharmacophore generation methods: sphingosine kinase 1 as case study. 39-62 - Solmaz Azimi, Joe Z. Wu, Sheenam Khuttan, Tom Kurtzman, Nanjie Deng, Emilio Gallicchio:
Application of the alchemical transfer and potential of mean force methods to the SAMPL8 host-guest blinded challenge. 63-76 - Ammar Abdo, Maude Pupin:
Turbo prediction: a new approach for bioactivity prediction. 77-85
Volume 36, Number 2, February 2022
- Jessie Low Gan, Dhruv Kumar, Cynthia Chen, Bryn C. Taylor, Benjamin R. Jagger, Rommie E. Amaro, Christopher T. Lee:
Benchmarking ensemble docking methods in D3R Grand Challenge 4. 87-99 - Franz Waibl, Johannes Kraml, Monica L. Fernández-Quintero, Johannes R. Loeffler, Klaus R. Liedl:
Explicit solvation thermodynamics in ionic solution: extending grid inhomogeneous solvation theory to solvation free energy of salt-water mixtures. 101-116 - Benjamin Ries, Karl Normak, R. Gregor Weiß, Salomé Rieder, Emília P. Barros, Candide Champion, Gerhard König, Sereina Riniker:
Relative free-energy calculations for scaffold hopping-type transformations with an automated RE-EDS sampling procedure. 117-130 - Parthajit Roy, Dhananjay Bhattacharyya:
Contact networks in RNA: a structural bioinformatics study with a new tool. 131-140 - Mengqi Cui, Kun Zhang, Ruihan Wu, Juan Du:
Exploring the interaction mechanism between antagonist and the jasmonate receptor complex by molecular dynamics simulation. 141-155
Volume 36, Number 3, March 2022
- Anita Rácz, Timothy B. Dunn, Dávid Bajusz, Taewon David Kim, Ramón Alain Miranda-Quintana, Károly Héberger:
Extended continuous similarity indices: theory and application for QSAR descriptor selection. 157-173 - Benjamin Ries, Salomé Rieder, Clemens Rhiner, Philippe H. Hünenberger, Sereina Riniker:
RestraintMaker: a graph-based approach to select distance restraints in free-energy calculations with dual topology. 175-192 - Qinfang Sun, Avik Biswas, R. S. K. Vijayan, Pierrick Craveur, Stefano Forli, Arthur J. Olson, Andres Emanuelli Castaner, Karen Kirby, Stefan G. Sarafianos, Nan-Jie Deng, Ronald M. Levy:
Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid. 193-203 - Nivedita Dutta, Indrajit Deb, Joanna Sarzynska, Ansuman Lahiri:
Data-informed reparameterization of modified RNA and the effect of explicit water models: application to pseudouridine and derivatives. 205-224 - Sangrak Lim, Yong Oh Lee, Juyong Yoon, Young Jun Kim:
Affinity prediction using deep learning based on SMILES input for D3R grand challenge 4. 225-235 - Itsuki Maeda, Akinori Sato, Shunsuke Tamura, Tomoyuki Miyao:
Ligand-based approaches to activity prediction for the early stage of structure-activity-relationship progression. 237-252 - Ignacio Aliagas, Alberto Gobbi, Man-Ling Lee, Benjamin D. Sellers:
Comparison of logP and logD correction models trained with public and proprietary data sets. 253-262
Volume 36, Number 4, April 2022
- Phillip S. Hudson, Félix Aviat, Rubén Meana-Pañeda, Luke C. Warrensford, Benjamin C. Pollard, Samarjeet Prasad, Michael R. Jones, H. Lee Woodcock III, Bernard R. Brooks:
Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches. 263-277 - Wijitra Meelua, Julianna Oláh, Jitrayut Jitonnom:
Role of water coordination at zinc binding site and its catalytic pathway of dizinc creatininase: insights from quantum cluster approach. 279-289 - Harold Grosjean, Mehtap Isik, Anthony Aimon, David L. Mobley, John D. Chodera, Frank von Delft, Philip C. Biggin:
SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction. 291-311 - Wei-Tse Hsu, Dominique A. Ramirez, Tarek Sammakia, Zhongping Tan, Michael R. Shirts:
Identifying signatures of proteolytic stability and monomeric propensity in O-glycosylated insulin using molecular simulation. 313-328
Volume 36, Number 5, May 2022
- Gerry Maggiora:
Is the reductionist paradox an Achilles Heel of drug discovery? 329-338 - Michael S. Lajiness:
The power of a mentor. 339-340 - José L. Medina-Franco, Norberto Sánchez-Cruz, Edgar López-López, Bárbara I. Díaz-Eufracio:
Progress on open chemoinformatic tools for expanding and exploring the chemical space. 341-354 - Raquel Rodríguez-Pérez, Jürgen Bajorath:
Evolution of Support Vector Machine and Regression Modeling in Chemoinformatics and Drug Discovery. 355-362 - Thomas Blaschke, Jürgen Bajorath:
Fine-tuning of a generative neural network for designing multi-target compounds. 363-371 - John H. Van Drie:
Hit diffusion: limitations to drug discovery and structure-based design. 373-379 - W. Patrick Walters:
Comparing classification models - a practical tutorial. 381-389 - Jeffrey K. Weber, Joseph A. Morrone, Sugato Bagchi, Jan D. Estrada Pabon, Seung-gu Kang, Leili Zhang, Wendy D. Cornell:
Simplified, interpretable graph convolutional neural networks for small molecule activity prediction. 391-404
Volume 36, Number 6, June 2022
- Faisal Malik, Zhijun Li:
Is there a common allosteric binding site for G-protein coupled receptors? 405-413 - Jinxing Li, Chao Li, Jun Sun, Vasile Palade:
RDPSOVina: the random drift particle swarm optimization for protein-ligand docking. 415-425 - Mei Qian Yau, Jason S. E. Loo:
Consensus scoring evaluated using the GPCR-Bench dataset: Reconsidering the role of MM/GBSA. 427-441 - Andrés Martínez Mora, Vigneshwari Subramanian, Filip Miljkovic:
Multi-task convolutional neural networks for predicting in vitro clearance endpoints from molecular images. 443-457 - Hemavathy Nagarajan, Ansar Samdani, Umashankar Vetrivel, Jeyaraman Jeyakanthan:
Deciphering the conformational transitions of LIMK2 active and inactive states to ponder specific druggable states through microsecond scale molecular dynamics simulation. 459-482
Volume 36, Number 7, July 2022
- Eleonora Proia, Alessio Ragno, Lorenzo Antonini, Manuela Sabatino, Milan Mladenovic, Roberto Capobianco, Rino Ragno:
Ligand-based and structure-based studies to develop predictive models for SARS-CoV-2 main protease inhibitors through the 3d-qsar.com portal. 483-505 - Sandeep Kumar, Rajendra Bhadane, Shruti Shandilya, Outi M. H. Salo-Ahen, Suman Kapila:
Identification of HPr kinase/phosphorylase inhibitors: novel antimicrobials against resistant Enterococcus faecalis. 507-520 - Jyoti Verma, Abdul Hasan, Sujatha Sunil, Naidu Subbarao:
In silico identification and in vitro antiviral validation of potential inhibitors against Chikungunya virus. 521-536 - Qiyang Wu, Tianyang Huang, Songyan Xia, Frank Otto, Tzong-Yi Lee, Hsien-Da Huang, Ying-Chih Chiang:
On the force field optimisation of β-lactam cores using the force field Toolkit. 537-547 - C. Ignacio Sainz-Díaz, Alexander Pérez de la Luz, Carolina Barrientos-Salcedo, Misaela Francisco-Marquez, Catalina Soriano-Correa:
Crystal polymorphism and spectroscopical properties of sulfonamides in solid state by means of First Principles calculations. 549-562
Volume 36, Number 8, August 2022
- Yujin Wu, Charles L. Brooks III:
Covalent docking in CDOCKER. 563-574 - Javier García-Marín, Diego Rodréguez-Puyol, Juan José Vaquero:
Insight into the mechanism of molecular recognition between human Integrin-Linked Kinase and Cpd22 and its implication at atomic level. 575-589 - Kai Zhu, Cui Li, Kingsley Y. Wu, Christopher Mohr, Xun Li, Brian Lanman:
Modeling receptor flexibility in the structure-based design of KRASG12C inhibitors. 591-604 - Maxence Delaunay, Tâp Ha-Duong:
Des3PI: a fragment-based approach to design cyclic peptides targeting protein-protein interactions. 605-621
Volume 36, Number 9, September 2022
- Veerabahu Shanmugasundaram, Jürgen Bajorath, Ralph E. Christoffersen, James D. Petke, W. Jeffrey Howe, Mark A. Johnson, Dimitris K. Agrafiotis, Pil Lee, Leslie A. Kuhn, Jay T. Goodwin, M. Katharine Holloway, Thompson N. Doman, W. Patrick Walters, Suzanne K. Schreyer, José L. Medina-Franco, Karina Martínez-Mayorga, Linda L. Restifo:
Epilogue to the Gerald Maggiora Festschrift: a tribute to an exemplary mentor, colleague, collaborator, and innovator. 623-638 - Patrick Penner, Virginie Y. Martiny, Louis Bellmann, Florian Flachsenberg, Marcus Gastreich, Isabelle Theret, Christophe Meyer, Matthias Rarey:
FastGrow: on-the-fly growing and its application to DYRK1A. 639-651 - Luz América Chi, Somayeh Asgharpour, José Correa-Basurto, Cindy Rodríguez Bandala, Marlet Martínez-Archundia:
Unveiling the G4-PAMAM capacity to bind and protect Ang-(1-7) bioactive peptide by molecular dynamics simulations. 653-675 - Jacob D. Durrant:
Prot2Prot: a deep learning model for rapid, photorealistic macromolecular visualization. 677-686 - Sergio A. Rodriguez, Jasmine Vy Tran, Spencer J. Sabatino, Andrew S. Paluch:
Predicting octanol/water partition coefficients and pKa for the SAMPL7 challenge using the SM12, SM8 and SMD solvation models. 687-705
Volume 36, Number 10, October 2022
- Martin Amezcua, Jeffry Setiadi, Yunhui Ge, David L. Mobley:
An overview of the SAMPL8 host-guest binding challenge. 707-734 - Xiao Liu, Lei Zheng, Chu Qin, John Z. H. Zhang, Zhaoxi Sun:
Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: I. Standard procedure. 735-752 - Andreas Tosstorff, Markus G. Rudolph, Jason C. Cole, Michael Reutlinger, Christian Kramer, Hervé Schaffhauser, Agnès Nilly, Alexander Flohr, Bernd Kuhn:
A high quality, industrial data set for binding affinity prediction: performance comparison in different early drug discovery scenarios. 753-765 - Yunhui Ge, Oliver J. Melling, Weiming Dong, Jonathan W. Essex, David L. Mobley:
Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo. 767-779
Volume 36, Number 11, November 2022
- Phasit Charoenkwan, Pramote Chumnanpuen, Nalini Schaduangrat, Pietro Lio', Mohammad Ali Moni, Watshara Shoombuatong:
Improved prediction and characterization of blood-brain barrier penetrating peptides using estimated propensity scores of dipeptides. 781-796 - Federica Agosta, Glen E. Kellogg, Pietro Cozzini:
From oncoproteins to spike proteins: the evaluation of intramolecular stability using hydropathic force field. 797-804 - Andreas H. Göller:
Reliable gas-phase tautomer equilibria of drug-like molecule scaffolds and the issue of continuum solvation. 805-824 - Rodrigo Ochoa, Pilar Cossio, Thomas Fox:
Protocol for iterative optimization of modified peptides bound to protein targets. 825-835
Volume 36, Number 12, December 2022
- Kiril Lanevskij, Remigijus Didziapetris, Andrius Sazonovas:
Physicochemical QSAR analysis of hERG inhibition revisited: towards a quantitative potency prediction. 837-849 - Roberto Paciotti, Cecilia Coletti, Alessandro Marrone, Nazzareno Re:
The FMO2 analysis of the ligand-receptor binding energy: the Biscarbene-Gold(I)/DNA G-Quadruplex case study. 851-866 - Ruifeng Liu, Srinivas Laxminarayan, Jaques Reifman, Anders Wallqvist:
Enabling data-limited chemical bioactivity predictions through deep neural network transfer learning. 867-878 - Xiao Liu, Lei Zheng, Yalong Cong, Zhihao Gong, Zhixiang Yin, John Z. H. Zhang, Zhirong Liu, Zhaoxi Sun:
Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: II. regression and dielectric constant. 879-894
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