Search results for "MM/PBSA"

Hits ?▲	Authors	Title	Venue	Year	Link	Author keywords
129	Jacob Kongsted, Ulf Ryde	An improved method to predict the entropy term with the MM/PBSA approach.	J. Comput. Aided Mol. Des.	2009	DBLP DOI BibTeX RDF	MM/PBSA, Avidin, Factor Xa, Cytochrome P450, Entropy
26	Yuchen Sun, Xibing He, Tingjun Hou, Lianjin Cai, Viet Hoang Man, Junmei Wang	Development and test of highly accurate endpoint free energy methods. 1: Evaluation of ABCG2 charge model on solvation free energy prediction and optimization of atom radii suitable for more accurate solvation free energy prediction by the PBSA method.	J. Comput. Chem.	2023	DBLP DOI BibTeX RDF
26	Yuchen Sun, Tingjun Hou, Xibing He, Viet Hoang Man, Junmei Wang	Development and test of highly accurate endpoint free energy methods. 2: Prediction of logarithm of n-octanol-water partition coefficient (logP) for druglike molecules using MM-PBSA method.	J. Comput. Chem.	2023	DBLP DOI BibTeX RDF
26	Anushka Mitra, Shibambika Manna, Raima Kundu, Ditipriya Hazra, Amlan Roychowdhury	Brute Force Virtual Drug Screening with Molecular Dynamics Simulation and MM/PBSA to Find Potent Inhibitors of METTL16.	IEEE ACM Trans. Comput. Biol. Bioinform.	2023	DBLP DOI BibTeX RDF
26	Harvinder Singh, Anupam Raja, Ajay Prakash, Bikash Medhi	Gmx_qk: An Automated Protein/Protein-Ligand Complex Simulation Workflow Bridged to MM/PBSA, Based on Gromacs and Zenity-Dependent GUI for Beginners in MD Simulation Study.	J. Chem. Inf. Model.	2023	DBLP DOI BibTeX RDF
26	Rimsha Yousaf, Afifa Navid, Syed Sikander Azam	Discovery of novel Glutaminase allosteric inhibitors through drug repurposing and comparative MMGB/PBSA and molecular dynamics simulation.	Comput. Biol. Medicine	2022	DBLP DOI BibTeX RDF
26	Maryam Ebrahimi, Leila Karami, Mahdi Alijanianzadeh	Computational repurposing approach for targeting the critical spike mutations in B.1.617.2 (delta), AY.1 (delta plus) and C.37 (lambda) SARS-CoV-2 variants using exhaustive structure-based virtual screening, molecular dynamic simulations and MM-PBSA methods.	Comput. Biol. Medicine	2022	DBLP DOI BibTeX RDF
26	Isanka Rajapaksha, Chanika Ruchini Mudalige, Dilini Karunarathna, Nisansa de Silva, Gathika Ratnayaka, Amal Shehan Perera	SigmaLaw PBSA - A Deep Learning Approach For Aspect Based Sentiment Analysis in Legal Opinion Texts.	J. Data Intell.	2022	DBLP DOI BibTeX RDF
26	Harutyun Sahakyan	Improving virtual screening results with MM/GBSA and MM/PBSA rescoring.	J. Comput. Aided Mol. Des.	2021	DBLP DOI BibTeX RDF
26	Yan-jing Sheng, Yue-wen Yin, Yu-Qing Ma, Hong-ming Ding	Improving the Performance of MM/PBSA in Protein-Protein Interactions via the Screening Electrostatic Energy.	J. Chem. Inf. Model.	2021	DBLP DOI BibTeX RDF
26	Andreia Fortuna, Paulo J. Costa	Optimized Halogen Atomic Radii for PBSA Calculations Using Off-Center Point Charges.	J. Chem. Inf. Model.	2021	DBLP DOI BibTeX RDF
26	Leonardo Bruno Federico, Guilherme Martins Silva, Suzane Quintana Gomes, Isaque Antonio Galindo Francischini, Mariana Pegrucci Barcelos, Cleydson Breno Rodrigues dos Santos, Luciano T. Costa, Joaquín María Campos Rosa, Carlos Henrique Tomich de Paula da Silva	Potential colchicine binding site inhibitors unraveled by virtual screening, molecular dynamics and MM/PBSA.	Comput. Biol. Medicine	2021	DBLP DOI BibTeX RDF
26	Isanka Rajapaksha, Chanika Ruchini Mudalige, Dilini Karunarathna, Nisansa de Silva, Amal Shehan Perera, Gathika Ratnayaka	Sigmalaw PBSA - A Deep Learning Model for Aspect-Based Sentiment Analysis for the Legal Domain.	DEXA (1)	2021	DBLP DOI BibTeX RDF
26	Mei Qian Yau, Abigail L. Emtage, Jason S. E. Loo	Benchmarking the performance of MM/PBSA in virtual screening enrichment using the GPCR-Bench dataset.	J. Comput. Aided Mol. Des.	2020	DBLP DOI BibTeX RDF
26	Panagiotis Lagarias, Kerry Barkan, Eva Tzortzini, Margarita Stampelou, Eleni Vrontaki, Graham Ladds, Antonios Kolocouris	Correction to Insights to the Binding of a Selective Adenosine A3 Receptor Antagonist using Molecular Dynamic Simulations, MM-PBSA and MM-GBSA Free Energy Calculations, and Mutagenesis.	J. Chem. Inf. Model.	2020	DBLP DOI BibTeX RDF
26	Mei Qian Yau, Abigail L. Emtage, Nathaniel J. Y. Chan, Stephen W. Doughty, Jason S. E. Loo	Evaluating the performance of MM/PBSA for binding affinity prediction using class A GPCR crystal structures.	J. Comput. Aided Mol. Des.	2019	DBLP DOI BibTeX RDF
26	Eko Aditya Rifai, Marc van Dijk, Nico P. E. Vermeulen, Arry Yanuar, Daan P. Geerke	A Comparative Linear Interaction Energy and MM/PBSA Study on SIRT1-Ligand Binding Free Energy Calculation.	J. Chem. Inf. Model.	2019	DBLP DOI BibTeX RDF
26	Panagiotis Lagarias, Kerry Barkan, Eva Tzortzini, Margarita Stampelou, Eleni Vrontaki, Graham Ladds, Antonios Kolocouris	Insights to the Binding of a Selective Adenosine A3 Receptor Antagonist Using Molecular Dynamic Simulations, MM-PBSA and MM-GBSA Free Energy Calculations, and Mutagenesis.	J. Chem. Inf. Model.	2019	DBLP DOI BibTeX RDF
26	Xiao Hu, Alessandro Contini	Rescoring Virtual Screening Results with the MM-PBSA Methods: Beware of Internal Dielectric Constants.	J. Chem. Inf. Model.	2019	DBLP DOI BibTeX RDF
26	Luan Carvalho Martins, Pedro Henrique Monteiro Torres, Renata Barbosa de Oliveira, Pedro Geraldo Pascutti, Elio A. Cino, Rafaela Salgado Ferreira	Investigation of the binding mode of a novel cruzain inhibitor by docking, molecular dynamics, ab initio and MM/PBSA calculations.	J. Comput. Aided Mol. Des.	2018	DBLP DOI BibTeX RDF
26	Yunhui Peng, Lexuan Sun, Zhe Jia, Lin Li 0003, Emil Alexov	Predicting protein-DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver.	Bioinform.	2018	DBLP DOI BibTeX RDF
26	Nicolas Chéron, Eugene I. Shakhnovich	Effect of sampling on BACE-1 ligands binding free energy predictions via MM-PBSA calculations.	J. Comput. Chem.	2017	DBLP DOI BibTeX RDF
26	Ido Y. Ben-Shalom, Stefania Pfeiffer-Marek, Karl-Heinz Baringhaus, Holger Gohlke	Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations.	J. Chem. Inf. Model.	2017	DBLP DOI BibTeX RDF
26	Chiduru Watanabe, Hirofumi Watanabe, Kaori Fukuzawa, Lorien J. Parker, Yoshio Okiyama, Hitomi Yuki, Shigeyuki Yokoyama, Hirofumi Nakano, Shigenori Tanaka, Teruki Honma	Theoretical Analysis of Activity Cliffs among Benzofuranone-Class Pim1 Inhibitors Using the Fragment Molecular Orbital Method with Molecular Mechanics Poisson-Boltzmann Surface Area (FMO+MM-PBSA) Approach.	J. Chem. Inf. Model.	2017	DBLP DOI BibTeX RDF
26	Joao Pedro do Vale Hipolito Cavalheiro, Nuno Miguel Matos Pires, Tao Dong 0006	MM-PBSA: Challenges and opportunities.	CISP-BMEI	2017	DBLP DOI BibTeX RDF
26	Xiao Liu, Jinfeng Liu 0004, Tong Zhu, Lujia Zhang, Xiao He 0004, John Z. H. Zhang	PBSA_E: A PBSA-Based Free Energy Estimator for Protein-Ligand Binding Affinity.	J. Chem. Inf. Model.	2016	DBLP DOI BibTeX RDF
26	Cristina Paissoni, Dimitrios Spiliotopoulos, Giovanna Musco, Andrea Spitaleri	GMXPBSA 2.1: A GROMACS tool to perform MM/PBSA and computational alanine scanning.	Comput. Phys. Commun.	2015	DBLP DOI BibTeX RDF
26	Pin-Chih Su, Cheng-Chieh Tsai, Shahila Mehboob, Kirk E. Hevener, Michael E. Johnson	Comparison of radii sets, entropy, QM methods, and sampling on MM-PBSA, MM-GBSA, and QM/MM-GBSA ligand binding energies of F. tularensis enoyl-ACP reductase (FabI).	J. Comput. Chem.	2015	DBLP DOI BibTeX RDF
26	Jianzhong Chen, Xingyu Wang, Tong Zhu, Qinggang Zhang, John Z. H. Zhang	A Comparative Insight into Amprenavir Resistance of Mutations V32I, G48V, I50V, I54V, and I84V in HIV-1 Protease Based on Thermodynamic Integration and MM-PBSA Methods.	J. Chem. Inf. Model.	2015	DBLP DOI BibTeX RDF
26	Marharyta Petukh, Minghui Li, Emil Alexov	Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method.	PLoS Comput. Biol.	2015	DBLP DOI BibTeX RDF
26	Cristina Paissoni, Dimitrios Spiliotopoulos, Giovanna Musco, Andrea Spitaleri	GMXPBSA 2.0: A GROMACS tool to perform MM/PBSA and computational alanine scanning.	Comput. Phys. Commun.	2014	DBLP DOI BibTeX RDF
26	Rashmi Kumari, Rajendra Kumar 0003, Andrew M. Lynn	g_mmpbsa - A GROMACS Tool for High-Throughput MM-PBSA Calculations.	J. Chem. Inf. Model.	2014	DBLP DOI BibTeX RDF
26	Yong-Liang Zhu, Paul Beroza, Dean R. Artis	Including Explicit Water Molecules as Part of the Protein Structure in MM/PBSA Calculations.	J. Chem. Inf. Model.	2014	DBLP DOI BibTeX RDF
26	Georgios Leonis, Thomas Steinbrecher, Manthos G. Papadopoulos	A Contribution to the Drug Resistance Mechanism of Darunavir, Amprenavir, Indinavir, and Saquinavir Complexes with HIV-1 Protease Due to Flap Mutation I50V: A Systematic MM-PBSA and Thermodynamic Integration Study.	J. Chem. Inf. Model.	2013	DBLP DOI BibTeX RDF
26	Tian Zhu, Hyun Lee, Hao Lei, Christopher Jones, Kavankumar Patel, Michael E. Johnson, Kirk E. Hevener	Fragment-Based Drug Discovery Using a Multidomain, Parallel MD-MM/PBSA Screening Protocol.	J. Chem. Inf. Model.	2013	DBLP DOI BibTeX RDF
26	Paulius Mikulskis, Samuel Genheden, Patrik Rydberg, Lars Sandberg, Lars Olsen, Ulf Ryde	Binding affinities in the SAMPL3 trypsin and host-guest blind tests estimated with the MM/PBSA and LIE methods.	J. Comput. Aided Mol. Des.	2012	DBLP DOI BibTeX RDF
26	Sameer Kawatkar, Demetri Moustakas, Matthew Miller, Diane Joseph-McCarthy	Virtual fragment screening: exploration of MM-PBSA re-scoring.	J. Comput. Aided Mol. Des.	2012	DBLP DOI BibTeX RDF
26	Hemant Kumar Srivastava, G. Narahari Sastry	Molecular Dynamics Investigation on a Series of HIV Protease Inhibitors: Assessing the Performance of MM-PBSA and MM-GBSA Approaches.	J. Chem. Inf. Model.	2012	DBLP DOI BibTeX RDF
26	Maria Safi, Ryan H. Lilien	Efficient a Priori Identification of Drug Resistant Mutations Using Dead-End Elimination and MM-PBSA.	J. Chem. Inf. Model.	2012	DBLP DOI BibTeX RDF
26	Allyn R. Brice, Brian N. Dominy	Analyzing the robustness of the MM/PBSA free energy calculation method: Application to DNA conformational transitions.	J. Comput. Chem.	2011	DBLP DOI BibTeX RDF
26	Matthias Negri, Maurizio Recanatini, Rolf W. Hartmann	Computational investigation of the binding mode of bis(hydroxylphenyl)arenes in 17β-HSD1: molecular dynamics simulations, MM-PBSA free energy calculations, and molecular electrostatic potential maps.	J. Comput. Aided Mol. Des.	2011	DBLP DOI BibTeX RDF
26	Tingjun Hou, Junmei Wang, Youyong Li, Wei Wang 0051	Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations.	J. Chem. Inf. Model.	2011	DBLP DOI BibTeX RDF
26	Giulio Rastelli, Alberto Del Rio 0001, Gianluca Degliesposti, Miriam Sgobba	Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA.	J. Comput. Chem.	2010	DBLP DOI BibTeX RDF
26	Wai Keat Yam, Habibah A. Wahab	Molecular Insights into 14-Membered Macrolides Using the MM-PBSA Method.	J. Chem. Inf. Model.	2009	DBLP DOI BibTeX RDF
26	David C. Thompson 0002, Christine Humblet, Diane Joseph-McCarthy	Investigation of MM-PBSA Rescoring of Docking Poses.	J. Chem. Inf. Model.	2008	DBLP DOI BibTeX RDF
26	Scott P. Brown, Steven W. Muchmore	Rapid Estimation of Relative Protein-Ligand Binding Affinities Using a High-Throughput Version of MM-PBSA.	J. Chem. Inf. Model.	2007	DBLP DOI BibTeX RDF
26	Christopher S. Page, Paul A. Bates	Can MM-PBSA calculations predict the specificities of protein kinase inhibitors?	J. Comput. Chem.	2006	DBLP DOI BibTeX RDF
26	Scott P. Brown, Steven W. Muchmore	High-Throughput Calculation of Protein-Ligand Binding Affinities: Modification and Adaptation of the MM-PBSA Protocol to Enterprise Grid Computing.	J. Chem. Inf. Model.	2006	DBLP DOI BibTeX RDF