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Literature of interest
Anthony J. Clark, Pratyush Tiwary, Ken Borrelli, Shulu Feng, Edward B. Miller, Robert Abel, Richard A. Friesner, and B. J. Berne. Prediction of Protein–Ligand Binding Poses via a Combination of Induced Fit Docking and Metadynamics Simulations. J. Chem. Theory Comput. DOI: 10.1021/acs.jctc.6b00201. Publication Date (Web): May 04, 2016.
Andrew Anighoro and Jürgen Bajorath. Three-Dimensional Similarity in Molecular Docking: Prioritizing Ligand Poses on the Basis of Experimental Binding Modes. J. Chem. Inf. Model. DOI: 10.1021/acs.jcim.5b00745. Publication Date (Web): February 26, 2016.
Matthew Patrick Baumgartner and Carlos J. Camacho. Choosing the Optimal Rigid Receptor for Docking and Scoring in the CSAR 2013/2014 Experiment. J. Chem. Inf. Model. DOI: 10.1021/acs.jcim.5b00338. Publication Date (Web): July 29, 2015.
Cen Gao, Nels Thorsteinson, Ian Watson, Jibo Wang, and Michal Vieth. Knowledge-Based Strategy to Improve Ligand Pose Prediction Accuracy for Lead Optimization. J. Chem. Inf. Model. DOI: 10.1021/acs.jcim.5b00186. Publication Date (Web): July 8, 2015.
Nathalie Lagarde, Jean-François Zagury, and Matthieu Montes. Benchmarking Data Sets for the Evaluation of Virtual Ligand Screening Methods: Review and Perspectives. J. Chem. Inf. Model. DOI: 10.1021/acs.jcim.5b00090. Publication Date (Web): June 18, 2015.
Koichi Tamura and Shigehiko Hayashi. Linear Response Path Following: A Molecular Dynamics Method To Simulate Global Conformational Changes of Protein upon Ligand Binding. J. Chem. Theory Comput. DOI: 10.1021/acs.jctc.5b00120. Publication Date (Web): June 15, 2015.
Joseph W. Kaus, Ed Harder, Teng Lin, Robert Abel, J. Andrew McCammon, and Lingle Wang. How To Deal with Multiple Binding Poses in Alchemical Relative Protein–Ligand Binding Free Energy Calculations. J. Chem. Theory Comput. DOI: 10.1021/acs.jctc.5b00214. Publication Date (Web): May 21, 2015.
Jie Liu and Renxiao Wang. Classification of Current Scoring Functions. J. Chem. Inf. Model. DOI: 10.1021/ci500731a. Publication Date (Web): February 19, 2015.
Hanieh Mirzaei, Shahrooz Zarbafian, Elizabeth Villar, Scott Mottarella, Dmitri Beglov, Sandor Vajda, Ioannis Ch. Paschalidis, Pirooz Vakili, and Dima Kozakov. Energy Minimization on Manifolds for Docking Flexible Molecules. J. Chem. Theory Comput. DOI: 10.1021/ct500155t. Publication Date (Web): February 13, 2015.
Tim ten Brink, Clémentine Aguirre, Thomas E. Exner and Isabelle Krimm. Performance of Protein–Ligand Docking with Simulated Chemical Shift Perturbations. J. Chem. Inf. Model. DOI: 10.1021/ci500446s. Publication Date (Web): October 30, 2014.
Prasad Chaskar, Vincent Zoete and Ute F. Röhrig. Toward On-The-Fly Quantum Mechanical/Molecular Mechanical (QM/MM) Docking: Development and Benchmark of a Scoring Function. J. Chem. Inf. Model. DOI: 10.1021/ci5004152. Publication Date (Web): October 9, 2014.
Eric Therrien, Nathanael Weill, Anna Tomberg, Christopher R. Corbeil, Devin Lee and Nicolas Moitessier. Docking Ligands into Flexible and Solvated Macromolecules. 7. Impact of Protein Flexibility and Water Molecules on Docking-Based Virtual Screening Accuracy. J. Chem. Inf. Model. DOI: 10.1021/ci500299h. Publication Date (Web): October 3, 2014.
Fabio Broccatelli and Nathan Brown. Best of Both Worlds: On the Complementarity of Ligand-Based and Structure-Based Virtual Screening. J. Chem. Inf. Model. DOI: 10.1021/ci5001604. Publication Date (Web): May 30, 2014.
Niels Hansen and Wilfred F van Gunsteren. Practical Aspects of Free-Energy Calculations: A Review. J. Chem. Theory Comput. DOI: 10.1021/ct500161f. Publication Date (Web): May 20, 2014.
Manuel Luitz and Martin Zacharias. Protein-ligand docking using Hamiltonian replica exchange simulations with soft core potentials. J. Chem. Inf. Model. DOI: 10.1021/ci500296f. Publication Date (Web): May 24, 2014.
Stefan Doerr and Gianni De Fabritiis. On-the-fly learning and sampling of ligand binding by high-throughput molecular simulations. J. Chem. Theory Comput. DOI: 10.1021/ct400919u. Publication Date (Web): March 26, 2014.
Pedro J. Ballester, Adrian Schreyer, and Tom L. Blundell. Does a more precise chemical description of protein-ligand complexes lead to more accurate prediction of binding affinity?. J. Chem. Inf. Model. DOI: 10.1021/ci500091r. Publication Date (Web): February 16, 2014.
Marc Adler and Paul Beroza. Improved Ligand Binding Energies Derived from Molecular Dynamics: Replicate Sampling Enhances the Search of Conformational Space. J. Chem. Inf. Model. DOI: 10.1021/ci400285z. Publication Date (Web): July 12, 2013.
James B. Dunbar, Richard Dayton Smith, Kelly L Damm-Ganamet, Aqeel Ahmed, Emilio Xavier Esposito, James Delproposto, Krishnapriya Chinnaswamy, You-Na Kang, Ginger Kubish, Jason E. Gestwicki, Jeanne A. Stuckey, and Heather Ann Carlson. CSAR Dataset Release 2012: Ligands, affinities, complexes, and docking decoys. J. Chem. Inf. Model. DOI: 10.1021/ci4000486. Publication Date (Web): April 25, 2013.
Alexey A. Zeifman et al. Alchemical FEP Calculations of Ligand Conformer Focusing in Explicit Solvent. J. Chem. Theory Comput. DOI: 10.1021/ct300796g. Publication Date (Web): January 07, 2013.
Sereina Riniker, Luzi J. Barandun, François Diederich, Oliver Krämer, Andreas Steffen, Wilfred F. van Gunsteren. Free enthalpies of replacing water molecules in protein binding pockets. J. Comput.-Aided. Mol. Des. DOI: 10.1007/s10822-012-9620-8. Cover date: December 1, 2012.
Dennis Manfred Krüger, Gisela Jessen, and Holger Gohlke. How good are state-of-the-art docking tools in predicting ligand binding modes in protein-protein interfaces? J. Chem. Inf. Model. DOI: 10.1021/ci3003599. Publication Date (Web): October 16, 2012.
JCAMD Special Issue: A snapshot in time: Docking Challenge. Volume 26, Number 6 / June 2012.
Richard Dayton Smith, Alaina L Engdahl, James B. Dunbar, and Heather Ann Carlson. Biophysical Limits of Protein-Ligand Binding. J. Chem. Inf. Model. DOI: 10.1021/ci200612f. Publication Date (Web): June 19, 2012.
Jong Young Joung, Ky-Youb Nam, Kwang-Hwi Cho, and Kyoung Tai No. Ligand Aligning Method for Molecular Docking: Alignment of Property-Weighted Vectors. J. Chem. Inf. Model. DOI: 10.1021/ci200501p. Publication Date (Web): April 3, 2012.
Oliver Korb, Tjelvar S. G. Olsson, Simon Bowden, Richard John Hall, Marcel L Verdonk, John W. Liebeschuetz, and Jason Cole. On the Potential and Limitations of Ensemble Docking. J. Chem. Inf. Model. DOI: 10.1021/ci2005934. Publication Date (Web): April 8, 2012.
Alessandra Nurisso, Juan Bravo, Pierre Alain Carrupt, and Antoine Daina. Molecular docking using the Molecular Lipophilicity Potential as hydrophobic descriptor: impact on GOLD docking performance. J. Chem. Inf. Model. DOI: 10.1021/ci200515g. Publication Date (Web): March 30, 2012.
Gyorgy G Ferenczy and Gyorgy M Keseru. Thermodynamics of fragment binding. J. Chem. Inf. Model. DOI: 10.1021/ci200608b. Publication Date (Web): March 29, 2012.
Emanuele Perola, Lee Herman, and Jonathan Weiss. Development of a rule-based method for the assessment of protein druggability. J. Chem. Inf. Model. DOI: 10.1021/ci200613b. Publication Date (Web): March 26, 2012.
Thomas Scior, Gary Tresadern, Andreas Bender, Jose Luis Medina-Franco, Karina Martinez-Mayorga, Thierry Langer, Karina Cuanalo-Contreras, and Dimitris K Agrafiotis. Recognizing Pitfalls in Virtual Screening: A Critical Review. J. Chem. Inf. Model. DOI: 10.1021/ci200528d. Publication Date (Web): March 21, 2012.
Miklos Feher and Chris Williams. Numerical errors and chaotic behavior in docking simulations. J. Chem. Inf. Model. DOI: 10.1021/ci200598m. Publication Date (Web): March 1, 2012.
Matthias Michael Dietzen, Andreas Hildebrandt, Elena Zotenko and Thomas Lengauer. On the Applicability of Elastic Network Normal Modes in Small-Molecule Docking. J. Chem. Inf. Model. DOI: 10.1021/ci2004847. Publication Date (Web): February 10, 2012.
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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