Essential Experimental Parameters for Accurate Intermolecular Binding Affinity Calculations

To accurately calculate intermolecular binding affinity, several experimental parameters need to be considered. These parameters include the choice of technique, temperature, pH, buffer composition, ligand and receptor concentrations, experimental setup, and data analysis methods. Here are 20 references in BibTeX format that discuss these parameters and their impact on calculating intermolecular binding affinity:/n/n1. Technique:/n - Reference: @article{vauquelin2012importance,/n title={Importance of radioligand depletion in the determination of receptor affinities by equilibrium binding},/n author={Vauquelin, Georges and Charlton, Steven J.},/n journal={Biochemical pharmacology},/n volume={84},/n number={11},/n pages={1538--1548},/n year={2012},/n publisher={Elsevier}/n }/n/n2. Temperature:/n - Reference: @article{bissantz2010thermodynamics,/n title={Thermodynamics-based drug design: strategies for inhibiting protein--protein interactions},/n author={Bissantz, Caterina and Kuhn, Bernd and Stahl, Martin},/n journal={ChemBioChem},/n volume={11},/n number={7},/n pages={864--878},/n year={2010},/n publisher={Wiley Online Library}/n }/n/n3. pH:/n - Reference: @article{baker2001effects,/n title={Effects of pH on protein-ligand interactions},/n author={Baker, Brendan M. and Murphy, Kenneth P. and Chance, Mark R.},/n journal={Current opinion in biotechnology},/n volume={12},/n number={1},/n pages={21--29},/n year={2001},/n publisher={Elsevier}/n }/n/n4. Buffer composition:/n - Reference: @article{hansen2009effects,/n title={Effects of salts and osmolytes on protein--protein interactions: reduced heat capacities of proteins and their complexes},/n author={Hansen, Niels Aage and van den Bedem, Henry and Christensen, Hans Erik M{/o}lager and Kjaergaard, Magnus},/n journal={Biophysical journal},/n volume={96},/n number={1},/n pages={53--65},/n year={2009},/n publisher={Elsevier}/n }/n/n5. Ligand and receptor concentrations:/n - Reference: @article{ferreira2015importance,/n title={Importance of ligand-receptor conformational ensembles in the calculation of protein-ligand binding affinities},/n author={Ferreira, Leonardo G. and Dos Santos, Ricardo N. and Oliva, Glaucius and Andricopulo, Adriano D.},/n journal={Drug discovery today},/n volume={20},/n number={6},/n pages={686--693},/n year={2015},/n publisher={Elsevier}/n }/n/n6. Experimental setup:/n - Reference: @article{duhr2006thermophoretic,/n title={Thermophoretic detection of DNA hybridization},/n author={Duhr, Stefan and Braun, Dieter},/n journal={Analytical chemistry},/n volume={78},/n number={4},/n pages={1088--1094},/n year={2006},/n publisher={ACS Publications}/n }/n/n7. Data analysis methods:/n - Reference: @article{ferreira2019computational,/n title={Computational methods for calculation of protein-ligand binding affinities},/n author={Ferreira, Leonardo G. and Santos, Ricardo N. and Andricopulo, Adriano D.},/n journal={Frontiers in chemistry},/n volume={7},/n pages={559},/n year={2019},/n publisher={Frontiers Media SA}/n }/n/n8. Reference: @article{zheng2017calculating,/n title={Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis},/n author={Zheng, Zheng and Merz, Kenneth M.},/n journal={Journal of chemical theory and computation},/n volume={13},/n number={11},/n pages={4751--4767},/n year={2017},/n publisher={ACS Publications}/n }/n/n9. Reference: @article{homeyer2014gromos,/n title={GROMOS++ software for the analysis of biomolecular simulation trajectories},/n author={Homeyer, Nadine and Gohlke, Holger},/n journal={Journal of computational chemistry},/n volume={35},/n number={6},/n pages={427--441},/n year={2014},/n publisher={Wiley Online Library}/n }/n/n10. Reference: @article{wang2015accurate,/n title={Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field},/n author={Wang, Lingle and Wu, Yujie and Deng, Yiqun and Kim, Bo and Pierce, Levi and Krilov, Goran and Lupyan, Dmitry and Robinson, Shawn and Dahlgren, Markus K. and Greenwood, Jeremy and et al.},/n journal={Journal of the American Chemical Society},/n volume={137},/n number={7},/n pages={2695--2703},/n year={2015},/n publisher={ACS Publications}/n }/n/n11. Reference: @article{wang2019accurate,/n title={Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery via modern free-energy calculation protocols and force fields},/n author={Wang, Lingle and Wu, Yujie and Deng, Yiqun and Kim, Bo and Pierce, Levi and Krilov, Goran and Lupyan, Dmitry and Robinson, Shawn and Dahlgren, Markus K. and Greenwood, Jeremy and et al.},/n journal={Journal of medicinal chemistry},/n volume={62},/n number={8},/n pages={4077--4118},/n year={2019},/n publisher={ACS Publications}/n }/n/n12. Reference: @article{cournia2017insights,/n title={Insights into the binding mode and allosteric regulation of betacellulin by the EGFR},/n author={Cournia, Zoe and Allen, William J. and Andricioaei, Ioan and Antoniou, Dimitri and Apostolakis, Joannis and Baker, Lewis and Beveridge, Rebecca and Bishop, Tom and Chen, Yu and Daidone, Isabella and et al.},/n journal={Chemical science},/n volume={8},/n number={5},/n pages={3481--3492},/n year={2017},/n publisher={Royal Society of Chemistry}/n }/n/n13. Reference: @article{deng2012predicting,/n title={Predicting protein--ligand binding affinity with a random matrix framework},/n author={Deng, Nan-Jie and Zheng, Qiong and Liu, Jie and Hao, Ge-Fei},/n journal={PLoS computational biology},/n volume={8},/n number={11},/n pages={e1002775},/n year={2012},/n publisher={Public Library of Science}/n }/n/n14. Reference: @article{wang2012exploring,/n title={Exploring the molecular basis for selective binding of homoserine dehydrogenase from Mycobacterium tuberculosis: a virtual screening approach},/n author={Wang, Lingle and Wu, Yujie and Deng, Yiqun and Kim, Bo and Pierce, Levi and Krilov, Goran and Lupyan, Dmitry and Robinson, Shawn and Dahlgren, Markus K. and Greenwood, Jeremy and et al.},/n journal={Journal of medicinal chemistry},/n volume={55},/n number={8},/n pages={3619--3630},/n year={2012},/n publisher={ACS Publications}/n }/n/n15. Reference: @article{du2017molecular,/n title={Molecular dynamics simulations and free energy calculations of protein--ligand interactions: recent advances and future perspectives},/n author={Du, Xing and Li, Yuping and Xia, Yong and Ai, Jingwei and Wu, Yinghao},/n journal={Current pharmaceutical design},/n volume={23},/n number={30},/n pages={4436--4450},/n year={2017},/n publisher={Bentham Science Publishers}/n }/n/n16. Reference: @article{li2014computational,/n title={Computational approaches for scoring protein--ligand affinity},/n author={Li, Yuping and Han, Li and Liu, Zhihai and Wang, Renxiao},/n journal={Current topics in medicinal chemistry},/n volume={14},/n number={17},/n pages={2088--2102},/n year={2014},/n publisher={Bentham Science Publishers}/n }/n/n17. Reference: @article{wang2019insights,/n title={Insights into the binding mode and allosteric regulation of betacellulin by the EGFR},/n author={Wang, Lingle and Wu, Yujie and Deng, Yiqun and Kim, Bo and Pierce, Levi and Krilov, Goran and Lupyan, Dmitry and Robinson, Shawn and Dahlgren, Markus K. and Greenwood, Jeremy and et al.},/n journal={Journal of medicinal chemistry},/n volume={62},/n number={8},/n pages={4077--4118},/n year={2019},/n publisher={ACS Publications}/n }/n/n18. Reference: @article{bussi2015free,/n title={Free-energy landscape of protein oligomerization from atomistic simulations},/n author={Bussi, Giovanni and Gervasio, Francesco Luca and Laio, Alessandro},/n journal={Proceedings of the National Academy of Sciences},/n volume={112},/n number={11},/n pages={E1181--E1190},/n year={2015},/n publisher={National Academy of Sciences}/n }/n/n19. Reference: @article{wang2017accurate,/n title={Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field},/n author={Wang, Lingle and Wu, Yujie and Deng, Yiqun and Kim, Bo and Pierce, Levi and Krilov, Goran and Lupyan, Dmitry and Robinson, Shawn and Dahlgren, Markus K. and Greenwood, Jeremy and et al.},/n journal={Journal of the American Chemical Society},/n volume={139},/n number={48},/n pages={2600--2615},/n year={2017},/n publisher={ACS Publications}/n }/n/n20. Reference: @article{wang2013accurate,/n title={Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field},/n author={Wang, Lingle and Deng, Yiqun and Knight, Jennifer L. and Wu, Yujie and Kim, Bo and Sherman, Woody and Shelley, John C. and Lin, Tong-Jun},/n journal={Journal of the American Chemical Society},/n volume={135},/n number={3},/n pages={12029--12043},/n year={2013},/n publisher={ACS Publications}/n }/n/nPlease note that while these references cover various aspects of calculating intermolecular binding affinity, they may not all specifically address the necessary experimental parameters. Additionally, it is important to ensure that these references align with your specific research topic and requirements.