e-Molecular shapes and properties

Due to recent computer technology advances, shape analysis has gained importance in all domains. In drug design and proteomics, molecular surfaces (van der Waals surface, solvent accessible surface, solvent excluded surface, polar surface area, electron density surface, separating surface, etc.), buried surfaces (gap, cleft, cavity, etc.) as well as shape properties of these surfaces, can be easily computed and visualized via the Internet. Freely available resources from the Internet for academic use, are reviewed.

[1]  Konrad Hinsen,et al.  The molecular modeling toolkit: A new approach to molecular simulations , 2000, J. Comput. Chem..

[2]  D Walther,et al.  WebMol--a Java-based PDB viewer. , 1997, Trends in biochemical sciences.

[3]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[4]  J. D. Elliott,et al.  Prediction of the Intestinal Absorption of Endothelin Receptor Antagonists Using Three Theoretical Methods of Increasing Complexity , 1999, Pharmaceutical Research.

[5]  Oleg V. Tsodikov,et al.  Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature , 2002, J. Comput. Chem..

[6]  J Devillers,et al.  e-Statistics for deriving QSAR models , 2002, SAR and QSAR in environmental research.

[7]  Matthias Keil,et al.  Characterisation of Protein-Ligand Interfaces: Separating Surfaces , 1998 .

[8]  Michel Petitjean,et al.  Geometric molecular similarity from volume‐based distance minimization: Application to saxitoxin and tetrodotoxin , 1995, J. Comput. Chem..

[9]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[10]  A J Hopfinger,et al.  Three-dimensional molecular shape analysis-quantitative structure-activity relationship of a series of cholecystokinin-A receptor antagonists. , 1994, Journal of medicinal chemistry.

[11]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[12]  E A Merritt,et al.  Raster3D: photorealistic molecular graphics. , 1997, Methods in enzymology.

[13]  K. B. Ward,et al.  Occluded molecular surface: Analysis of protein packing , 1995, Journal of molecular recognition : JMR.

[14]  R C Wade,et al.  MolSurfer: two-dimensional maps for navigating three-dimensional structures of proteins. , 1999, Trends in biochemical sciences.

[15]  Pieter F. W. Stouten,et al.  Fast prediction and visualization of protein binding pockets with PASS , 2000, J. Comput. Aided Mol. Des..

[16]  Ramaswamy Nilakantan,et al.  New method for rapid characterization of molecular shapes: applications in drug design , 1993, J. Chem. Inf. Comput. Sci..

[17]  J D Gans,et al.  Qmol: a program for molecular visualization on Windows-based PCs. , 2001, Journal of molecular graphics & modelling.

[18]  K. Sharp,et al.  Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons , 1991, Proteins.

[19]  D. E. Clark Rapid calculation of polar molecular surface area and its application to the prediction of transport phenomena. 1. Prediction of intestinal absorption. , 1999, Journal of pharmaceutical sciences.

[20]  A. Olson,et al.  Approximation and characterization of molecular surfaces , 1993, Biopolymers.

[21]  R C Wade,et al.  Analytically defined surfaces to analyze molecular interaction properties. , 1996, Journal of molecular graphics.

[22]  L. T. Ten Eyck,et al.  Rapid atomic density methods for molecular shape characterization. , 2001, Journal of molecular graphics & modelling.

[23]  M Rahman,et al.  WinMGM: a fast CPK molecular graphics program for analyzing molecular structure. , 1994, Journal of molecular graphics.

[24]  P. Selzer,et al.  Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties. , 2000, Journal of medicinal chemistry.

[25]  G Vriend,et al.  WHAT IF: a molecular modeling and drug design program. , 1990, Journal of molecular graphics.

[26]  Ioan Motoc,et al.  Molecular Shape Descriptors , 1983, Steric Effects in Drug Design.

[27]  A. Hopfinger A QSAR investigation of dihydrofolate reductase inhibition by Baker triazines based upon molecular shape analysis , 1980 .

[28]  Werner Braun,et al.  Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules , 1998, J. Comput. Chem..

[29]  M. Sanner,et al.  Reduced surface: an efficient way to compute molecular surfaces. , 1996, Biopolymers.

[30]  Irwin D. Kuntz,et al.  A fast and efficient method for 2D and 3D molecular shape description , 1992, J. Comput. Aided Mol. Des..

[31]  P Argos,et al.  Hydrophobic regions on protein surfaces: definition based on hydration shell structure and a quick method for their computation. , 1996, Protein engineering.

[32]  F. Eisenhaber Hydrophobic regions on protein surfaces , 1999 .

[33]  F E Blaney,et al.  Molecular surface comparison. 2. Similarity of electrostatic vector fields in drug design. , 1995, Journal of molecular graphics.

[34]  M. L. Connolly Solvent-accessible surfaces of proteins and nucleic acids. , 1983, Science.

[35]  Frank Eisenhaber,et al.  Improved strategy in analytic surface calculation for molecular systems: Handling of singularities and computational efficiency , 1993, J. Comput. Chem..

[36]  Chris Sander,et al.  The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies , 1995, J. Comput. Chem..

[37]  Robert B. Hermann,et al.  OVID and SUPER: Two overlap programs for drug design , 1991, J. Comput. Aided Mol. Des..

[38]  R. Laskowski SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. , 1995, Journal of molecular graphics.

[39]  A. Olson,et al.  Shape analysis of molecular surfaces , 1993, Biopolymers.

[40]  B. Masek,et al.  Molecular shape comparison of angiotensin II receptor antagonists. , 1993, Journal of medicinal chemistry.