Water PMF for predicting the properties of water molecules in protein binding site
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Hualiang Jiang | Mingyue Zheng | Bing Xiong | Jingkang Shen | Yanlian Li | Hualiang Jiang | Jingkang Shen | M. Zheng | B. Xiong | Yanlian Li
[1] J. Finney,et al. Water? What's so special about it? , 2004, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.
[2] Pengyu Y. Ren,et al. Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation , 2003 .
[3] Fumio Hirata,et al. Potential of Mean Force between Two Molecular Ions in a Polar Molecular Solvent: A Study by the Three-Dimensional Reference Interaction Site Model , 1999 .
[4] Julien Michel,et al. Prediction of the water content in protein binding sites. , 2009, The journal of physical chemistry. B.
[5] Yasuomi Kiyota,et al. A New Approach for Investigating the Molecular Recognition of Protein: Toward Structure-Based Drug Design Based on the 3D-RISM Theory. , 2011, Journal of chemical theory and computation.
[6] P. Ball. Water as an active constituent in cell biology. , 2008, Chemical reviews.
[7] T. Lazaridis. Inhomogeneous Fluid Approach to Solvation Thermodynamics. 1. Theory , 1998 .
[8] Song Liu,et al. A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes. , 2005, Journal of medicinal chemistry.
[9] Fumio Hirata,et al. Placevent: An algorithm for prediction of explicit solvent atom distribution—Application to HIV‐1 protease and F‐ATP synthase , 2012, J. Comput. Chem..
[10] G. Klebe,et al. Knowledge-based scoring function to predict protein-ligand interactions. , 2000, Journal of molecular biology.
[11] Fumio Hirata,et al. Water molecules in a protein cavity detected by a statistical-mechanical theory. , 2005, Journal of the American Chemical Society.
[12] Norio Yoshida,et al. Selective ion binding by protein probed with the statistical mechanical integral equation theory. , 2007, The journal of physical chemistry. B.
[13] Ken A Dill,et al. Modeling water, the hydrophobic effect, and ion solvation. , 2005, Annual review of biophysics and biomolecular structure.
[14] Sheldon Park,et al. Statistical and molecular dynamics studies of buried waters in globular proteins , 2005, Proteins.
[15] Y. Martin,et al. A general and fast scoring function for protein-ligand interactions: a simplified potential approach. , 1999, Journal of medicinal chemistry.
[16] A. Sali,et al. Statistical potential for assessment and prediction of protein structures , 2006, Protein science : a publication of the Protein Society.
[17] Fumio Hirata,et al. Locating missing water molecules in protein cavities by the three‐dimensional reference interaction site model theory of molecular solvation , 2006, Proteins.
[18] Benoît Roux,et al. An Integral Equation To Describe the Solvation of Polar Molecules in Liquid Water , 1997 .
[19] Renxiao Wang,et al. Analysis of Ligand-Bound Water Molecules in High-Resolution Crystal Structures of Protein-Ligand Complexes , 2007, J. Chem. Inf. Model..
[20] Greg L. Hura,et al. Small-angle scattering and the structure of ambient liquid water , 2010, Proceedings of the National Academy of Sciences.
[21] Jing Li,et al. Knowledge-Based Scoring Functions in Drug Design: 3. A Two-Dimensional Knowledge-Based Hydrogen-Bonding Potential for the Prediction of Protein-Ligand Interactions , 2011, J. Chem. Inf. Model..
[22] Huynh-Hoa Bui,et al. WATGEN: An algorithm for modeling water networks at protein–protein interfaces , 2007, J. Comput. Chem..
[23] Norio Yoshida,et al. Selective ion-binding by protein probed with the 3D-RISM theory. , 2006, Journal of the American Chemical Society.
[24] Gerhard Klebe,et al. DSX: A Knowledge-Based Scoring Function for the Assessment of Protein-Ligand Complexes , 2011, J. Chem. Inf. Model..
[25] Guoli Wang,et al. PISCES: a protein sequence culling server , 2003, Bioinform..
[26] Jing Li,et al. Knowledge-Based Scoring Functions in Drug Design: 2. Can the Knowledge Base Be Enriched? , 2011, J. Chem. Inf. Model..
[27] Pietro Cozzini,et al. Robust classification of "relevant" water molecules in putative protein binding sites. , 2008, Journal of medicinal chemistry.
[28] Themis Lazaridis,et al. Water at biomolecular binding interfaces. , 2007, Physical chemistry chemical physics : PCCP.
[29] B. Berne,et al. Role of the active-site solvent in the thermodynamics of factor Xa ligand binding. , 2008, Journal of the American Chemical Society.
[30] Fumio Hirata,et al. Ligand mapping on protein surfaces by the 3D-RISM theory: toward computational fragment-based drug design. , 2009, Journal of the American Chemical Society.
[31] Ricardo L. Mancera,et al. WaterScore: a novel method for distinguishing between bound and displaceable water molecules in the crystal structure of the binding site of protein-ligand complexes , 2003, Journal of molecular modeling.
[32] Hongyi Zhou,et al. Distance‐scaled, finite ideal‐gas reference state improves structure‐derived potentials of mean force for structure selection and stability prediction , 2002, Protein science : a publication of the Protein Society.
[33] P. Wernet,et al. The Structure of the First Coordination Shell in Liquid Water , 2004, Science.
[34] Themis Lazaridis,et al. Thermodynamic contributions of the ordered water molecule in HIV-1 protease. , 2003, Journal of the American Chemical Society.
[35] T. M. Raschke,et al. Water structure and interactions with protein surfaces. , 2006, Current opinion in structural biology.
[36] W. Punch,et al. Predicting conserved water-mediated and polar ligand interactions in proteins using a K-nearest-neighbors genetic algorithm. , 1997, Journal of molecular biology.
[37] Caterina Barillari,et al. Classification of water molecules in protein binding sites. , 2007, Journal of the American Chemical Society.
[38] Renxiao Wang,et al. Comparative evaluation of 11 scoring functions for molecular docking. , 2003, Journal of medicinal chemistry.
[39] Hualiang Jiang,et al. Knowledge-Based Scoring Functions in Drug Design. 1. Developing a Target-Specific Method for Kinase-Ligand Interactions , 2010, J. Chem. Inf. Model..
[40] I. Muegge,et al. Residence Times and Lateral Diffusion of Water at Protein Surfaces: Application to BPTI , 1995 .
[41] Teresa Head-Gordon,et al. The structure of ambient water , 2010 .