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Journal 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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