adding references

Author: skfegan

docs/science.rst

@@ -1,34 +1,42 @@
 Multiscale Cell Correlation Theory
 ==================================
 
-This section is to describe the scientific theory behind the methods used in CodeEntropy.
+This section is to describe the scientific theory behind the method used in CodeEntropy.
 
-The multiscale cell correlation (MCC) method [1,2] has been developed in the group of Richard Henchman to calculate entropy from molecular dynamics (MD) simulations. It has been applied to liquids [3], proteins [4], and water [5].
-The purpose of this project is to develop a unified, well written and well tested code that would enable users from any group to calculate the entropy from their simulations using the MCC method. The latest code can be found at github.com/ccpbiosim/codeentropy.
+The multiscale cell correlation (MCC) method [1-3] has been developed in the group of Richard Henchman to calculate entropy from molecular dynamics (MD) simulations. 
+It has been applied to liquids [1,3,4], proteins [2,5,6], solutions [6-9], and complexes [6,7].
+The purpose of this project is to develop and release well written code that enables users from any group to calculate the entropy from their simulations using the MCC. 
+The latest code can be found at github.com/ccpbiosim/codeentropy.
 
 The method requires forces to be written to the MD trajectory files along with the coordinates.
 
 Key References
 --------------
-[1] Ulf Hensen, Frauke Grater, and Richard H. Henchman. “Macromolecular
-Entropy Can Be Accurately Computed from Force”. In: Journal of Chemi-
-cal Theory and Computation 10 (2014), pp. 4777–4781.
+[1] Richard H. Henchman. "Free energy of liquid water from a computer simulation via cell theory". In: Journal of Chemical Physics 126 (2007), 064504.
 
-[2] Jonathan Higham et al. “Entropy of Flexible Liquids from Hierarchical
+[2] Ulf Hensen, Frauke Grater, and Richard H. Henchman. “Macromolecular
+Entropy Can Be Accurately Computed from Force”. In: Journal of Chemical Theory and Computation 10 (2014), pp. 4777–4781.
+
+[3] Jonathan Higham et al. “Entropy of Flexible Liquids from Hierarchical
 Force-Torque Covariance and Coordination”. In: Molecular Physics 116
 (2018), pp. 1965–1976.
 
-[3] Hafiz Saqib Ali, Jonathan Higham, and Richard H. Henchman. “Entropy
+[4] Hafiz Saqib Ali, Jonathan Higham, and Richard H. Henchman. “Entropy
 of Simulated Liquids Using Multiscale Cell Correlation”. In: Entropy 21
 (2019), p. 750.
 
-[4] Arghya Chakravorty, Jonathan Higham, and Richard H. Henchman. “En-
+[5] Arghya Chakravorty, Jonathan Higham, and Richard H. Henchman. “En-
 tropy of Proteins Using Multiscale Cell Correlation”. In: J. Chem. Inf.
 Model. 60 (2020), pp. 5540–5551.
 
-[5] Jas Kalayan et al. “Total Free Energy Analysis of Fully Hydrated Proteins”.
+[6] Jas Kalayan et al. “Total Free Energy Analysis of Fully Hydrated Proteins”.
 In: Proteins 91 (2023), pp. 74–90.
 
+[7] Hafiz Saqib Ali et al."Energy-entropy method using Multiscale Cell Correlation to calculate binding free energies in the SAMPL8 Host-Guest Challenge". In: Journal of Computer Aided Molecular Design 35 (2021), 911-921.
+
+[8] Fabio Falcioni et al. "Energy-entropy prediction of octanol-water logP of SAMPL7 N-acylsulfonamide bioisosters". In Journal of Computer Aided Molecular Design 35 (2021) 831-840.
+
+[9] Hafiz Saqib Ali et al. "Energy-entropy Multiscale Cell Correlation method to predict toluene–water log P in the SAMPL9 challenge". In Physical Chemistry Chemical Physics 25 (2023), 27524-27531.
 
 Hierarchy
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