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Literature of interest
Jožica Dolenc, Sereina Riniker, Roberto Gaspari, Xavier Daura and Wilfred F. van Gunsteren. Free energy calculations offer insights into the influence of receptor flexibility on ligand–receptor binding affinities. J. Comput.-Aided. Mol. Des. Volume 25, Number 8, 709-716, DOI: 10.1007/s10822-011-9453-x. Accepted: June 20, 2011.
Jožica Dolenc, Sereina Riniker, Roberto Gaspari, Xavier Daura and Wilfred F. van Gunsteren. Free energy calculations offer insights into the influence of receptor flexibility on ligand–receptor binding affinities. J. Comput.-Aided. Mol. Des. Volume 25, Number 8, 709-716, DOI: 10.1007/s10822-011-9453-x. Accepted: June 20, 2011.
Sergey A. Samsonov, Joan Teyra and M. Teresa Pisabarro. Docking glycosaminoglycans to proteins: analysis of solvent inclusion. J. Comput.-Aided. Mol. Des. Volume 25, Number 5, 477-489, DOI: 10.1007/s10822-011-9433-1. Accepted: May 6, 2011.
Christian Kramer and Peter Gedeck. Three Descriptor Model sets a High Standard for the CSAR-NRC HiQ benchmark. J.Chem.Inf.Model. DOI: 10.1021/ci200030h, Publication Date (Web): May 30, 2011.
Fedor Novikov, Alexey Zeifman, Oleg Stroganov, Viktor Stroylov, Val Kulkov, and Ghermes Chilov. CSAR scoring challenge reveals the need for new concepts in estimating protein-ligand binding affinity. J. Chem. Inf. Model. DOI: 10.1021/ci200034y, Publication Date (Web): May 25, 2011.
Pedro Ballester and John Mitchell. Comments on “Leave-Cluster-Out Cross-Validation is appropriate for scoring functions derived from diverse protein data sets”: Significance for the validation of scoring functions. J. Chem. Inf. Model. DOI: 10.1021/ci200057e, Publication Date (Web): May 18, 2011.
Yan Li, Yuan Zhao, Zhihai Liu, and Renxiao Wang. Automatic Tailoring and Transplanting: A Practical Method that Makes Virtual Screening More Useful. J. Chem. Inf. Model. DOI: 10.1021/ci200036m, Publication Date (Web): April 26, 2011.
Zheng, Zh. and M. Merz, Jr. K. Ligand Identification Scoring Algorithm (LISA). J. Chem. Inf. Model. DOI: 10.1021/ci2000665, Publication Date (Web): May 11, 2011.
Raman, E.P.; Yu, W.; Guvench, O.; MacKerell, Jr. A.D. Reproducing Crystal Binding Modes of Ligand Functional Groups Using Site-Identification by Ligand Competitive Saturation (SILCS) Simulations. J. Chem. Inf. Model., 2011, 51 (4), pp 877–896. DOI: 10.1021/ci100462t, Publication Date (Web): April 1, 2011.
Lie, M.A.; Thomsen, R; Pedersen, C.N.S.; Schiøtt, B.; Christensen, M.H. Molecular Docking with Ligand Attached Water Molecules. J. Chem. Inf. Model., 2011, 51 (4), pp 909–917. DOI: 10.1021/ci100510m, Publication Date (Web): March 31, 2011.
Kramer, C.; Gedeck, P. Global Free Energy Scoring Functions Based on Distance-Dependent Atom-Type Pair Descriptors. J. Chem. Inf. Model., 2011, 51 (3), pp 707–720. DOI: 10.1021/ci100473d, Publication Date (Web): February 22, 2011.
Xu, M; Lill, M. Significant Enhancement of Docking Sensitivity Using Implicit Ligand Sampling. J. Chem. Inf. Model., 2011, 51 (3), pp 693–706. DOI: 10.1021/ci100457t, Publication Date (Web): March 4, 2011.
McGann, M. FRED Pose Prediction and Virtual Screening Accuracy. J. Chem. Inf. Model., 2011, 51 (3), pp 578–596. DOI: 10.1021/ci100436p, Publication Date (Web): February 16, 2011.
Wallach, I; Lilien, R. Virtual Decoy Sets for Molecular Docking Benchmarks. J. Chem. Inf. Model., 2011, 51 (2), pp 196–202. DOI: 10.1021/ci100374f, Publication Date (Web): January 5, 2011.
Niijima, S; Yabuuchi, H; Okuno, Y. Cross-Target View to Feature Selection: Identification of Molecular Interaction Features in Ligand−Target Space. J. Chem. Inf. Model., 2011, 51 (1), pp 15–24. DOI: 10.1021/ci1001394, Publication Date (Web): December 10, 2010.
Strino, F; Lii, Jenn-Huei; Koppisetty, C; Nyholm, P-G; Gabius, H-J. Selenoglycosides in silico: ab initio-derived reparameterization of MM4, conformational analysis using histo-blood group ABH antigens and lectin docking as indication for potential of bioactivity. J. Comput.-Aided. Mol. Des., Volume 24, Number 12, 1009-1021, DOI: 10.1007/s10822-010-9392-y.
Burger, S; Thompson, D; Ayers, P. Quantum Mechanics/Molecular Mechanics Strategies for Docking Pose Refinement: Distinguishing between Binders and Decoys in Cytochrome c Peroxidase. J. Chem. Inf. Model., 2011, 51 (1), pp 93–101. DOI: 10.1021/ci100329z, Publication Date (Web): December 6, 2010.
Thangapandian, S; John, S; Sakkiah, S; Woo Lee, K. Molecular Docking and Pharmacophore Filtering in the Discovery of Dual-Inhibitors for Human Leukotriene A4 Hydrolase and Leukotriene C4 Synthase. J. Chem. Inf. Model., 2011, 51 (1), pp 33–44. DOI: 10.1021/ci1002813, Publication Date (Web): December 6, 2010.
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