Chemistry Reference
In-Depth Information
109. Velec HF, Gohlke H, Klebe G (2005) DrugScore(CSD)-knowledge-based scoring function
derived from small molecule crystal data with superior recognition rate of near-native ligand
poses and better affinity prediction. J Med Chem 48(20):6296-6303
110. Kortagere S, Krasowski MD, Ekins S (2009) The importance of discerning shape in molecu-
lar pharmacology. Trends Pharmacol Sci 30(3):138-147
111. McGann MR et al (2003) Gaussian docking functions. Biopolymers 68(1):76-90
112. Stark JL et al (2010) Solution structure and function of YndB, an AHSA1 protein from
Bacillus subtilis. Proteins 78(16):3328-3340
113. Merlitz H, Herges T, Wenzel W (2004) Fluctuation analysis and accuracy of a large-scale in
silico screen. J Comput Chem 25(13):1568-1575
114. Tirado-Rives J, Jorgensen WL (2006) Contribution of conformer focusing to the uncertainty
in predicting free energies for protein-ligand binding. J Med Chem 49(20):5880-5884
115. Charifson PS et al (1999) Consensus scoring: a method for obtaining improved hit rates from
docking databases of three-dimensional structures into proteins. J Med Chem 42(25):
5100-5109
116. Peng JW (2009) Communication breakdown: protein dynamics and drug design. Structure
17(3):319-320
117. Hayward S, de Groot BL (2008) Normal modes and essential dynamics. Methods Mol Biol
443:89-106 (Molecular Modeling of Proteins)
118. Huang SY, Zou X (2007) Ensemble docking of multiple protein structures: considering
protein structural variations in molecular docking. Proteins 66(2):399-421
119. Erickson JA et al (2004) Lessons in molecular recognition: the effects of ligand and protein
flexibility on molecular docking accuracy. J Med Chem 47(1):45-55
120. Sherman W et al (2006) Novel procedure for modeling ligand/receptor induced fit effects.
J Med Chem 49(2):534-553
121. Stark J, Powers R (2008) Rapid protein-ligand costructures using chemical
shift
perturbations. J Am Chem Soc 130(2):535-545
122. B-Rao C, Subramanian J, Sharma SD (2009) Managing protein flexibility in docking and its
applications. Drug Discov Today 14(7-8):394-400
123. Jiang F, Kim SH (1991) “Soft docking”: matching of molecular surface cubes. J Mol Biol 219
(1):79-102
124. Claussen H et al (2001) FlexE: efficient molecular docking considering protein structure
variations. J Mol Biol 308(2):377-395
125. Alberts IL, Todorov NP, Dean PM (2005) Receptor flexibility in de novo ligand design
and docking. J Med Chem 48(21):6585-6596
126. Barril X, Morley SD (2005) Unveiling the full potential of flexible receptor docking
using multiple crystallographic structures. J Med Chem 48(13):4432-4443
127. Klebe G (2006) Virtual
ligand screening:
strategies, perspectives and limitations.
Drug Discov Today 11(13-14):580-594
128. Schneider G, Bohm HJ (2002) Virtual screening and fast automated docking methods.
Drug Discov Today 7(1):64-70
129. Chen H et al (2006) On evaluating molecular-docking methods for pose prediction and
enrichment factors. J Chem Inf Model 46(1):401-415
130. Kontoyianni M, McClellan LM, Sokol GS (2004) Evaluation of docking performance:
comparative data on docking algorithms. J Med Chem 47(3):558-565
131. Kirchmair J et al (2008) Evaluation of the performance of 3D virtual screening protocols:
RMSD comparisons, enrichment assessments, and decoy selection-what can we learn from
earlier mistakes? J Comput Aided Mol Des 22(3-4):213-228
132. Bender A, Glen RC (2005) A discussion of measures of enrichment in virtual screening:
comparing the information content of descriptors with increasing levels of sophistication.
J Chem Inf Model 45(5):1369-1375
133. Truchon J-F, Bayly CI (2007) Evaluating virtual screening methods: good and bad metrics for
the “early recognition” problem. J Chem Inf Model 47(2):488-508
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