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Biomedical subjects

T E Ferrin

Publications and source records attributed to T E Ferrin.

10 recordsLinked to original sources
PubMed1998

The object technology framework: an object-oriented interface to molecular data and its application to collagen.

We describe the Object Technology Framework (OTF) software system developed at the University of California, San Francisco Computer Graphics Laboratory for creating C+2 classes that facilitate rapid biomolecular application development and the application of the OTF to collagen modeling. C+2 class libraries for accessing and manipulating data from standard scientific data sources can be generated using the program genlib and its class library toolkit Molecule, thereby facilitating development of new applications. Use of the OTF for generating ideal collagen structural models (gencollagen) is described. The source code for the OTF is freely available at http:/(/)www.cgl.ucsf.edu/off/ to interested application developers.

Collagen↗
PubMed1995

Annotating PDB files with scene information.

We have implemented extensions to the Brookhaven Protein Data Bank (PDB) file format for incorporating scene information such as viewing parameters, additional molecular information (e.g., van der Waals radii and atom colors), and user-defined graphics. These extensions were made in conformance with the PDB standard and provide sufficient information to render the scene in various styles such as space-filling images and ribbon diagrams. For the past 5 years these extensions have been used in the MidasPlus molecular modeling system and have proved both powerful and sufficient for generating complex molecular images. We propose that the extensions to the PDB presented here be adopted by the molecular modeling community for incorporation into visualization programs.

Computer Graphics↗
PubMed1992

Automated site-directed drug design using molecular lattices.

Receptor-based drug design is predicated on the knowledge of the structure of a target receptor and the principles of molecule recognition. The objective is to produce a wide diversity of structures that are sterically and electrostatically complementary to a specified receptor site. Many drug-receptor interactions are controlled by a few key receptor groups. This observation leads to a design approach in which one focuses on chemical fragments that putatively interact with the key receptor groups. There then remains the difficult task of joining the fragments into molecular structures that match the spatial patterns of recognition forces in the receptor site. In this paper, we describe a new modeling program, BUILDER, that combines database searching techniques and structure generation algorithms within an interactive graphics modeling environment (MidasPlus). A novel tool for process communication (delegate) is introduced and examples of its use are given. To demonstrate the functionality of the package and its ability to produce novel structures, we examine the active site of HIV-1 protease.

Algorithms↗
PubMed1991

Conic: a fast renderer for space-filling molecules with shadows.

We present an algorithm for generating images of molecules represented as a set of intersecting opaque spheres. Both perspective and shadows are computed to provide realistic visual cues. Compared to existing programs for generating similar images, our algorithm is both more accurate and several times faster. We present in detail the mathematics used in picture generation, along with examples of the computed images.

Algorithms↗
PubMed1991

An affordable approach to interactive desktop molecular modeling.

The amazing revolution in computer hardware performance and cost reduction has yet to be carried over to computer software. In fact, application software today is often more expensive and less reliable than the hardware. New enhancements in software development techniques, such as object oriented programming and interactive graphics based user interface design, finally may be having a significant impact on the time-to-market and reliability of these application programs. We discuss our experiences using one such set of software development tools available on the NeXT workstation and describe the effort required to port our MidasPlus molecular modeling package to the NeXT work-station.

Computer Graphics↗
PubMed1991

Molecular structure and dynamics of tricyclic antidepressant drugs.

The molecular structure, electrostatic potentials and dynamics of imipramine, chlorimipramine, amitriptyline and nortriptyline were examined by computer graphics, molecular mechanical energy calculations and molecular dynamics simulations, using the AMBER all atom force field. Starting coordinates for amitriptyline and nortriptyline were generated by model building from the crystal structure of imipramine. The structures were refined by molecular mechanical energy minimization, and used as starting points for molecular dynamics simulations in vacuo and in aqueous solution. The simulations demonstrated considerable flexibility of the molecules, both in the side chain and in the ring system, where the angle between the phenyl rings varied between 90 degrees and 168 degrees. The most frequently observed conformations of imipramine, chlorimipramine and nortriptyline during the simulations had the side chain folded above one of the phenyl rings, while amitriptyline showed both folded and extended side chain conformations during the simulations. The results may provide increased understanding of the molecular recognition and specificity of tricyclic antidepressant drugs in interaction with neurotransmitter receptor molecules.

Antidepressive Agents, Tricyclic↗
PubMed1990

A real-time malleable molecular surface.

We describe a method for generating a molecular surface using a parametric patch representation. Unlike previous methods, this algorithm generates a parametric patch surface which is smooth and G continuous and manipulable in real-time. Crucial to our approach is the creation of a net of approximately equilateral triangles from which we generate the control points used as the basis for describing the surface. We present in detail the method used for generating the triangular net and accompanying control points, along with examples of the resulting surfaces.

Algorithms↗
PubMed1982

Computer graphics in drug design: molecular modeling of thyroid hormone-prealbumin interactions.

Computer graphics modeling of the thyroxine-prealbumin complex provides a detailed picture of the interactions between thyroxine and prealbumin. A wide variety of thyroid hormone analogue-prealbumin complexes were modeled by calculating the molecular surfaces of the analogues and the prealbumin hormone-binding site. Analogues with high binding affinity were observed to fill more of the hormone-binding site than low-affinity analogues. These surface models described many aspects of the hormone-protein interaction which were not obvious using simple wire models and led us to develop a model which accounts for thyroid hormone-prealbumin structure-activity relationships and ultimately to predict and measure the relative binding affinities of four previously untested thyroid hormone analogues to prealbumin.

Chemical Phenomena↗
PubMed1981

Real-time color graphics in studies of molecular interactions.

Studies of the structures and interactions of large biological molecules require both coordinate data and three-dimensional visualization. Orthodox molecular models often bear a tenuous relationship to the coordinate data. In contrast, computer graphics requires that the display directly and accurately represent the data, and storage of modified configurations and recovery of original structures are simple. Software has been developed that allows real-time display of color line and surface displays of several interacting molecules, while quantitatively monitoring the stereochemistry.

Carboxypeptidases↗