Discovery Studio Scientific References

Browse References by Application Area

 

Protein Modeling and Sequence Analysis Biopolymer Buliding and Analysis Simulations Structure-Based Design

Ligand-Based Design Pharmacophore Modeling and Analysis QSAR and Library Design ADMET

 

Protein Modeling and Sequence Analysis

1. Spassov, V., Yan, L. and Flook, P. “The Dominant Role of Side-chain Backbone Interactions in Structural Realization of Amino-acid Code. ChiRotor: a Side-chain Prediction Algorithm Based on Side-chain Backbone Interactions,” Protein Science , 2007
2. Marti-Renom, M. A., Madhusudhan, M. S. and Sali, A., “Alignment of protein sequences by their profiles”, Protein Science , 2004 , 13 , 1071–1087
3. Eswar, N., Eramian, D., Webb, B., Shen, M., Sali. A. Protein Structure Modeling With MODELLER. Current Protocols in Bioinformatics John Wiley & Sons, Inc. , 2006, Supplement 15 , 5.6.1-5.6.30
4. Li L, Chen R (joint first authors), Weng Z, RDOCK: Refinement of Rigid-body Protein Docking Predictions. Proteins , 2003 , 53 , 693–707
5. Chen R, Li L, Weng Z, ZDOCK: An Initial-stage Protein-Docking Algorithm. Proteins, 2003 , 52 , 80 – 87
6. Morea, V., Lesk, A., and Tramontano, A. “Antibody Modeling: Implications for Engineering and Design,” METHODS , 2000 , 20 , 267.
7. Sali, A., Pottertone, L., Yuan, F., van Vlijmen, H., and Karplus, M., “Evaluation of comparative protein modeling by MODELLER,” Proteins , 1995 , 23 , 318.
8. Brooks,B.R.,Bruccoleri,R.E.,Olafson,B.D.,States,D.J.,Swaminathan,S.,and Karplus, M., “CHARMM: A program for macromolecular energy, minimization, and dynamics calculations,” J. Comput. Chem. , 1983 , 4 , 187-217.
   

Biopolymer Building and Analysis

1. Honig, B., Sharp, K., Yang, A.S., J. Phys. Chem. , 1993 , 97 , 1101.
2. Nicholls, A., and Honig, B., J. Comp. Chem. , 1991 , 12 , 435.
3. Sharp, B., Nichols, A., Friedman, R., and Honig, B., Biochemistry , 1991 , 30 , 9686.
   

Simulations

1. Spassov, VZ, et al. “The dominant role of side-chain backbone interactions in structural realization of amino acid code. ChiRotor: a side-chain prediction algorithm based on side-chain backbone interactions”, Protein Sci. , 2007 , 16(3) , 494-506.
2. Nimlos, MR at al. “Molecular modeling suggests induced fit of Family I carbohydrate-binding modules with a broken-chain cellulose surface”, Protein Eng. Des. Sel. , 2007 , 20(4) , 179-87.
3. Foloppe, N. et al. ”Structure-based design of novel Chk1 inhibitors: insights into hydrogen bonding and protein-ligand affinity” J. Med. Chem. , 2005 , 48(13) , 4332-45.
4. Spassov, VZ, et al. “LOOPER: A Molecular Mechanics Based Algorithm for Protein Loop Prediction”, Accepted, Protein Engineering, Design and Selection
   

Structure-Based Design

1. Yu, H. et al. “The discovery of novel vascular endothelial growth factor receptor tyrosine kinases inhibitors: pharmacophore modeling, virtual screening and docking studies” Chem Biol Drug Des. , 2007 , 69(3) , 204-11
2. Sato, H. Et al. “Prediction of multiple binding modes of the CDK2 inhibitors, anilinopyrazoles, using the automated docking programs GOLD, FlexX, and LigandFit: an evaluation of performance”, J Chem Inf Model. , 2006 , 46(6), 2552-62.
3. Warren G.L., et al. “A critical assessment of docking programs and scoring functions”, J. Med. Chem., 2006 , 49 , 5912.
4. Rao et al, J. Chem. Inf. Model (submitted)
5. Warren, GL et al. “A critical assessment of docking programs and scoring functions”, J. Med. Chem . 2006 , 49(20) , 5912-31.
6. Erickson et al. J Med Chem . 2004 , 47(1), 45-55.
   

Receptor-Ligand Interactions

Ligandfit

1. Taha, M.O., and AlDamen, M.A., "Effects of Variable Docking Conditions and Scoring Functions on Corresponding Protein-Aligned Comparative Molecular Field Analysis Models Constructed from Diverse Human Protein Tyrosine Phosphatase 1B Inhibitors," J. Med. Chem., 2005 , 48 , 8016-8034.
2. Taha, M.O., Qandil, A.M., Zaki, D.D., and AlDamen, M.A., "Ligand-Based Assessment of Factor Xa Binding Site Flexibility via Elaborate Pharmacophore Exploration and Genetic Algorithm-Based QSAR Modeling," Eur. J. Med. Chem. , 2005 , 40 , 701-727.
3. Triballeau, N., Acher, F., Brabet, I. , Pin, J.-P., and Bertrand, H.-O., "Virtual Screening Workflow Development Guided by the 'Receiver Operating Characteristic' Curve Approach. Application to High-Throughput Docking on Metabotropic Glutamate Receptor Subtype 4," J. Med. Chem. , 2005 , 48 , 2534-2547.
4. Kontoyianni, M., McClellan, L.M., and Sokol, G.S., "Evaluation of Docking Performance: Comparative Data on Docking Algorithms," J. Med. Chem. , 2004 , 47 , 558-565. (LigandFit/LigandScore)
5. Kroemer, R.T., Vulpetti, A., McDonald, J.J., Rohrer , D.C. , Trosset, J.Y., et al ., "Assessment of Docking Poses: Interactions-Based Accuracy Classification (IBAC) versus Crystal Structure Deviations," J. Chem. Inf. Comput. Sci. , 2004 , 44 871-881. (LigandFit/LigandScore)
6. Asano, T., Yoshikawa, T., Usui, T., Yamamoto, H., Yamamoto, Y., et al ., "Benzamides and Benzamidines as Specific Inhibitors of Epidermal Growth Factor Receptor and v-Src Protein Tyrosine Kinases," Bioorg. Med. Chem. , 2004 , 12 , 3529-3542. (LigandFit/LigandScore)
7. Gouldson, P.R., Kidley , N.J. , Bywater, R.P., Psaroudakis, G., Brooks, H.D., et al ., "Toward the Active Conformations of Rhodopsin and the ß2-Adrenergic Receptor," Proteins , 2004 , 56 , 67-84. (LigandFit/LigandScore)
8. Krovat, E.M., and Langer, T., "Impact of Scoring Functions on Enrichment in Docking-Based Virtual Screening: An Application Study on Renin Inhibitors," J. Chem. Inf. Comput. Sci. , 2004 , 44 , 1123-1129. (LigandFit/LigandScore)
9. Varady, J., Wu, X., Fang, X., Min, J., Hu, Z., et al ., "Molecular Modeling of the Three-Dimensional Structure of Dopamine 3 (D3) Subtype Receptor: Discovery of Novel and Potent D3 Ligands through a Hybrid Pharmacophore- and Structure-Based Database Searching Approach," J. Med. Chem. , 2003 , 46 , 4377-4392. (LigandFit/LigandScore)
10. Wang, R., Lu, Y., and Wang, S., "Comparative Evaluation of 11 Scoring Functions for Molecular Docking," J. Med. Chem. , 2003 , 46 , 2287-2303. (LigandFit/LigandScore)
11. Venkatachalam, C.M., Jiang, X., Oldfield, T., and Waldman, M.,"LigandFit: A Novel Method for the Shape-Directed Rapid Docking of Ligands to Protein Active Sites," J. Mol. Graph. Modell. , 2003 , 21 , 289-307. (LigandFit/LigandScore)
12. Bertrand, H.O., Bessis, A.S., Pin, J.P., and Acher, F.C., "Common and Selective Molecular Determinants Involved in Metabotopic Glutamate Receptor Agonist Activity," J. Med. Chem. , 2002 , 45 , 3171-3183.
13. Xu, R.X., Hassell, A.M., Vanderwall, D., Lambert, M.H., Holmes, W.D., et al ., "Atomic Structure of PDE4: Insights Into Phosphodiesterase Mechanism and Specificity," Science , 2000 , 288 , 1822-1825. (LigandFit/LigandScore)

LigandScore

1. Cotesta, S., Giordanetto, F., Trosset, J.-Y., Crivori, P., Kroemer, R. T., Stouten, P. F.W. and Vulpetti, A., “Virtual Screening to Enrich a Compound Collection with CDK2 Inhibitors Using Docking, Scoring, and Composite Scoring Models," Proteins: Struct., Funct., Bioinf. , 2005 , 60 , 629-643.

Ludi

1. Grembecka, J., Mucha, A., Cierpicki, T., and Kafarski, P. "The Most Potent Organophosphorus Inhibitors of Leucine Aminopeptidase. Structure-Based Design, Chemistry, and Activity," J. Med. Chem. , 2003 , 46 , 2641-2655.
2. Ji, H., Zhang, W., Zhang, M., Kudo, M., Aoyama, Y., Yoshida, Y., Sheng, C., Song, Y., Yang, S., Zhou, Y., Lu, J., and Zhu, J., "Structure-Based de Novo Design, Synthesis, and Biological Evaluation of Non-Azole Inhibitors Specific for Lanosterol 14r-Demethylase of Fungi," J. Med. Chem. , 2003 , 46 , 474-485.
3. Jorgensen, F.S., Christensen, I.T., Johansen, B.N., and Terp, G.E., "A New Concept for Multidimensional Selection of Ligand Conformations (MultiSelect) and Multidimensional Scoring (MultiScore) of Protein-Ligand Binding Affinities," J. Med. Chem. , 2001 , 44 , 2333-2343.
4. Kubinyi, H., "Chance Favors the Prepared Mind-from Serendipity to Rational Drug Design," J. Recept. Signal Transduction , 1999 , 19 , 15-35.
5. Muegge, I. , and Martin, Y.C., "A General and Fast Scoring Function for Protein-Ligand Interactions: A Simplified Potential Approach," J. Med. Chem. , 1999 , 42 , 791-804.
6. Böhm, H.-J.,"Prediction of Binding Constants of Protein Ligands: a Fast Method for the Prioritization of Hits Obtained from de Novo Design or 3D Database Search Programs," J. Comput.-Aided Mol. Des. , 1998 , 4 , 309-323.
7. Böhm, H.-J., "Towards the Automatic Design of Synthetically Accessible Protein Ligands: Peptides, Amides and Peptidomimetics," J. Comput.-Aided Mol. Des. , 1996 , 4 , 265-272.
8. Böhm, H.-J., "On the Use of Ludi to Search the Fine Chemicals Directory for Ligands of Proteins of Known Three-Dimensional Structure," J. Comput.-Aided Mol. Des. , 1994 , 5 , 623-632.
9. Böhm, H.-J., "The Development of a Simple Empirical Scoring Function to Estimate the Binding Constant for a Protein-Ligand Complex of Known Three-Dimensional Sturcture," J. Comput.-Aided Mol. Des. , 1994 , 3 , 243-256.
10. Böhm, H.-J., "A Novel Computational Tool for Automated Structure-Based Drug Design," J. Mol. Recognit. , 1993 , 3 , 131-137.
11. Böhm, H.-J., "Ludi: Rule-Based Automatic Design of New Substituents for Enzyme Inhibitor Leads," J. Comput.-Aided Mol. Des. , 1992 , 6 , 593-606.
12. Böhm, H.-J., "The Computer Program Ludi: a New Method for the de Novo Design of Enzyme Inhibitors," J. Comput.-Aided Mol. Des. , 1992 , 1 , 61-78.
    

Pharmacophore Modeling and Analysis

1. Purushottamachar P., et al., “First pharmacophore-based identification of androgen receptor down-regulating agents: discovery of potent anti-prostate cancer agents,” Bioorg Med Chem., 2007 , 15 , 3413-21.
2. Taha MO , et al., “Discovery of new potent human protein tyrosine phosphatase inhibitors via pharmacophore and QSAR analysis followed by in silico screening,” J Mol Graph Model. , 2007 , 25 , 870-84.
3. Agrafiotis, DK, et al., “Conformational Sampling of Bioactive Molecules: A Comparative Study,” J. Chem. Inf. Model. , 2007 , 47(3) , 1067-86
   

QSAR and Library Design

1. Cheg, D. et al., “Relationship of quantitative structure and pharmacokinetics in fluoroquinolone antibacterials”, World J Gastroenterol , 2007 , 13(17) , 2496-503
2. Jiang FC., et al., “The design and synthesis of 2-aminothiazole derivatives and their inhibitory activity on apoptosis”, Yao Xue Xue Bao , 2006 , 41(8) , 727-34
3. Bednarczyk D., et al., “Influence of molecular structure on substrate binding to the human organic cation transporter, hOCT”, Mol. Pharmacol , 2003 , 63(3) , 489-98
   

ADMET

1. Egan,W. J., Merz, K.M., Jr., and Baldwin, J. J., J. Med. Chem. , 2000 , 43 , 3867-3877.
2. Prentis, R.A., Lis, Y., and Walker, S.R., Br. J. Clin. Pharmac. , 1988 , 25 , 387-396.
3. Ghose, A. K.,Viswanadhan, V. N., Wendoloski, J. J., J. Phys. Chem. , 1998 , 102 , 3762-3772.