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- Group Seminar and Journal Club 2017 - NEW!
- Group Seminar and Journal Club 2016 - NEW!
- Group Seminars and Journal Clubs - 2016
- Installing PyMol from MacPorts
- How to calculate ROC curves
- MIPGen
- Small Molecule Dihedrals Parametrization
- Gaussian 09 and Antechamber12
- Organic solvent boxes
- Parametrize new ligands for AMBER and CHARMM
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2008. Induction effects in metal cation-benzene complexes. Physical chemistry chemical physics : PCCP. 10(19):2616-2624. Abstract
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2003. Theoretical studies on the inhibition mechanism of cyclooxygenase-2. Is there a unique recognition site? Journal of medicinal chemistry. 46(8):1372-1382. Abstract
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2000. DNA-triplex stabilizing properties of 8-aminoguanine. Nucleic acids research. 28(22):4531-4539. Abstract
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1999. Role of sugar re-puckering in the transition of A and B forms of DNA in solution. A molecular dynamics study. Journal of Biomolecular Structure & Dynamics. 17(1):89-99. Abstract
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1999. Can G-C Hoogsteen-wobble pairs contribute to the stability of d(G. C-C) triplexes? Nucleic acids research. 27(11):2248-2255. Abstract
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2014. Mechanistic insight into the enzymatic reduction of truncated hemoglobin N of Mycobacterium tuberculosis: Role of the CD loop and Pre-A motif in electron cycling. Journal of Biological Chemistry. 289
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2007. Inhibition of the heat shock protein 90 molecular chaperone in vitro and in vivo by novel, synthetic, potent resorcinylic pyrazole/isoxazole amide analogues. Molecular cancer therapeutics. 6(4):1198-1211. Abstract
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2009. Binding site detection and druggability index from first principles. Journal of medicinal chemistry. 52(8):2363-2371. Abstract
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2012. Allosteric regulation of PKCθ: understanding multistep phosphorylation and priming by ligands in AGC kinases.. Proteins. 80(1):269-80. Abstract
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2007. How solvent controls electronic energy transfer and light harvesting. Journal of Physical Chemistry B. 111(25):6978-6982. Abstract
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2010. Large-Scale Comparison of Four Binding Site Detection Algorithms. Journal of Chemical Information and Modeling.
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2010. Understanding and predicting druggability. A high-throughput method for detection of drug binding sites. Journal of medicinal chemistry. 53:5858-5867. Abstract
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2011. Shielded Hydrogen Bonds as Structural Determinants of Binding Kinetics: Application in Drug Design. Journal of the American Chemical Society. Abstract
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2011. MDpocket : Open Source Cavity Detection and Characterization on Molecular Dynamics Trajectories. Bioinformatics (Oxford, England). Abstract
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2012. Expanding the Target Space : Druggability Assessments. 44:302-318.
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2010. Fpocket: Online Tools for Protein Ensemble Pocket Detection and Tracking. Nucleic acids research. Abstract
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2002. Fast estimation of hydrogen-bonding donor and acceptor propensities: a GMIPp study. Journal of computer-aided molecular design. 16(8-9):569-583. Abstract
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2007. Towards a molecular scale interpretation of excitation energy transfer in solvated bichromophoric systems. II. The through-bond contribution. Journal of Physical Chemistry B. 111(4):853-863. Abstract
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2014. Polythiazole linkers as functional rigid connectors: A new RGD cyclopeptide with enhanced integrin selectivity. Chemical Science. 5
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2014. rDock: a fast, versatile and open source program for docking ligands to proteins and nucleic acids.. PLoS computational biology. 10(4):e1003571-e1003571. Abstract
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2003. QSAR study of dual cyclooxygenase and 5-lipoxygenase inhibitors 2,6-di-tert-butylphenol derivatives. Bioorganic & medicinal chemistry. 11(19):4207-4216. Abstract
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1993. QSAR and conformational analysis of the antiinflammatory agent amfenac and analogues. Journal of computer-aided molecular design. 7(2):183-198. Abstract
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2006. G-quadruplexes can maintain their structure in the gas phase. Journal of the American Chemical Society. 128(11):3608-3619. Abstract
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2002. A theoretical investigation on the effect of remote amino groups in hydrogen bonding of nucleic acids. Biopolymers. 61(1):52-60. Abstract