Comparative Molecular Field Analysis (CoMFA)

Abbreviations 3D D three-dimensional; C D molar concentration of a drug; CBG D corticosteroid binding globulin; CoMFA D comparative molecular field analysis; CoMSIA D comparative molecular similarity indices analysis; GOLPE D generating optimal linear PLS estimations; PLS D partial least squares; PRESS D predictive residual sum of squares; RMS D root mean squares; TBG D testosterone binding globulin.

[1]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[2]  F. Young.  Biochemistry , 1955, The Indian Medical Gazette.

[3]  Y. Martin,et al.  Quantitative drug design , 1978 .

[4]  J. Gasteiger,et al.  ITERATIVE PARTIAL EQUALIZATION OF ORBITAL ELECTRONEGATIVITY – A RAPID ACCESS TO ATOMIC CHARGES , 1980 .

[5]  Manfred E. Wolff,et al.  Burger's Medicinal chemistry , 1980 .

[6]  D. E. Patterson,et al.  Crossvalidation, Bootstrapping, and Partial Least Squares Compared with Multiple Regression in Conventional QSAR Studies , 1988 .

[7]  R. Cramer,et al.  Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. , 1988, Journal of the American Chemical Society.

[8]  Matthew Clark,et al.  Comparative molecular field analysis (CoMFA). 2. Toward its use with 3D-structural databases , 1990 .

[9]  S J Oatley,et al.  Crystal structures of Escherichia coli dihydrofolate reductase: the NADP+ holoenzyme and the folate.NADP+ ternary complex. Substrate binding and a model for the transition state. , 1990, Biochemistry.

[10]  Simon K. Kearsley,et al.  An alternative method for the alignment of molecular structures: Maximizing electrostatic and steric overlap , 1990 .

[11]  G E Kellogg,et al.  Allosteric modifiers of hemoglobin. 2. Crystallographically determined binding sites and hydrophobic binding/interaction analysis of novel hemoglobin oxygen effectors. , 1991, Journal of medicinal chemistry.

[12]  R. Cramer.  Partial Least Squares (PLS): Its strengths and limitations , 1993 .

[13]  Matthew Clark,et al.  The Probability of Chance Correlation Using Partial Least Squares (PLS) , 1993 .

[14]  H. Kubinyi.  QSAR: Hansch Analysis and Related Approaches: Kubinyi/QSAR , 1993 .

[15]  S. Wold,et al.  The kernel algorithm for PLS , 1993 .

[16]  Garland R. Marshall,et al.  3D-QSAR of angiotensin-converting enzyme and thermolysin inhibitors: A comparison of CoMFA models based on deduced and experimentally determined active site geometries , 1993 .

[17]  A. Good,et al.  Structure-activity relationships from molecular similarity matrices. , 1993, Journal of medicinal chemistry.

[18]  H. Kubinyi.  QSAR : Hansch analysis and related approaches , 1993 .

[19]  Richards Wg,et al.  QSAR's from similarity matrices. Technique validation and application in the comparison of different similarity evaluation methods. , 1993 .

[20]  Bruce L. Bush,et al.  Sample-distance partial least squares: PLS optimized for many variables, with application to CoMFA , 1993, J. Comput. Aided Mol. Des..

[21]  E. J. Ariëns.  Nonchiral, homochiral and composite chiral drugs. , 1993, Trends in pharmacological sciences.

[22]  G Klebe,et al.  On the prediction of binding properties of drug molecules by comparative molecular field analysis. , 1993, Journal of medicinal chemistry.

[23]  G. Klebe,et al.  Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity. , 1994, Journal of medicinal chemistry.

[24]  C. Braak,et al.  Comments on the PLS kernel algorithm , 1994 .

[25]  S. Wold,et al.  A PLS kernel algorithm for data sets with many variables and fewer objects. Part 1: Theory and algorithm , 1994 .

[26]  Han Van De Waterbeemd.  Advanced Computer-Assisted Techniques in Drug Discover , 1994 .

[27]  Gerhard Klebe,et al.  Different approaches toward an automatic structural alignment of drug molecules: Applications to sterol mimics, thrombin and thermolysin inhibitors , 1994, J. Comput. Aided Mol. Des..

[28]  G Greco,et al.  Effects of variable selection on CoMFA coefficient contour maps in a set of triazines inhibiting DHFR , 1994, J. Comput. Aided Mol. Des..

[29]  H. Kubinyi.  [The key to the castle. II. Hansch analysis, 3d-QSAR and de novo design]. , 1994, Pharmazie in unserer Zeit.

[30]  Gerhard Klebe,et al.  Recommendations for CoMFA Studies and 3D QSAR Publications , 1994 .

[31]  Exploring QSAR. , 1995, Environmental science & technology.

[32]  A Tropsha,et al.  Cross-validated R2-guided region selection for comparative molecular field analysis: a simple method to achieve consistent results. , 1995, Journal of medicinal chemistry.

[33]  Romano T. Kroemer,et al.  A new procedure for improving the predictiveness of CoMFA models and its application to a set of dihydrofolate reductase inhibitors , 1995, J. Comput. Aided Mol. Des..

[34]  Han van de Waterbeemd,et al.  Chemometric methods in molecular design , 1995 .

[35]  G R Marshall,et al.  3D-QSAR: a current perspective. , 1995, Trends in pharmacological sciences.

[36]  S. Wold,et al.  A PLS kernel algorithm for data sets with many variables and few objects. Part II: Cross‐validation, missing data and examples , 1995 .

[37]  A. C. Good,et al.  3D molecular similarity indices and their application in QSAR studies , 1995 .

[38]  Edgar F. Meyer,et al.  Backward binding and other structural surprises , 1995 .

[39]  M. Charton.  Advances in quantitative structure-property relationships , 1996 .

[40]  P. Goodford.  Multivariate characterization of molecules for QSAR analysis , 1996 .

[41]  Ulf Norinder,et al.  Single and domain mode variable selection in 3D QSAR applications , 1996 .

[42]  D. Hoekman.  Exploring QSAR Fundamentals and Applications in Chemistry and Biology, Volume 1. Hydrophobic, Electronic and Steric Constants, Volume 2 J. Am. Chem. Soc. 1995, 117, 9782 , 1996 .

[43]  Thomas Lengauer,et al.  Time-efficient flexible superposition of medium-sized molecules , 1997, German Conference on Bioinformatics.

[44]  Han van de Waterbeemd,et al.  Lipophilicity in drug action and toxicology , 1996 .

[45]  Han van de Waterbeemd,et al.  Lipophilicity in Drug Action and Toxicology: Pliška/Lipophilicity , 1996 .

[46]  Han van de Waterbeemd,et al.  Computer-Assisted Lead Finding and Optimization , 1997 .

[47]  C. Lemmen,et al.  FLEXS: a method for fast flexible ligand superposition. , 1998, Journal of medicinal chemistry.

[48]  Johann Gasteiger,et al.  Superposition of Three-Dimensional Chemical Structures Allowing for Conformational Flexibility by a Hybrid Method , 1998, J. Chem. Inf. Comput. Sci..

[49]  H. Kubinyi,et al.  Three-dimensional quantitative similarity-activity relationships (3D QSiAR) from SEAL similarity matrices. , 1998, Journal of medicinal chemistry.

[50]  Gerd Folkers,et al.  Pharmacokinetic optimization in drug research , 2001 .

[51]  A. Tropsha,et al.  Beware of q2! , 2002, Journal of molecular graphics & modelling.

[52]  H. Kubinyi,et al.  3D QSAR in drug design. , 2002 .

[53]  Phillip Jeffrey,et al.  The Practice of Medicinal Chemistry , 2004 .

[54]  Aaas News,et al.  Book Reviews , 1893, Buffalo Medical and Surgical Journal.