You are here: Home » Content

Browse by Author: Hernan Stamati

View author profile
Return to Browsing Content | Search for Content
Sort by: Results per page:
View: Detail | Compact | Statistics
[1] 2 Next 9 »
Geometric Methods in Structural Computational Biology (col10344)
Maintainers: Lydia E. Kavraki, David Schwarz, Hernan Stamati, Amarda Shehu
Institution: Rice University
Keywords: analysis of protein motion, area and volume of proteins, distance measures for proteins, geometric algorithms in biology, geometric methods in structural biology, motif identification in proteins, probablistic roadmap methods, protein classification, protein flexibility, protein functional annotation, protein modeling, robotics methods for protein modeling, structural computational biology
Summary: This course is a short series of lectures on Structural Computational Biology, with an emphasis on geometric algorithms. Topics covered include basic data structures for modeling proteins; kinematics and inverse kinematics of protein chains; distance measures and alignment algorithms for protein structures; motif finding for the functional annotation of proteins ... useful feedback.
Subject: Science and Technology
Language: English
Popularity: 82.76%
Revised: 2007-06-11
Revisions: 6
Assignment 1: Visualization and Ranking of Protein Conformations (m11615)
Maintainers: Lydia E. Kavraki, Amarda Shehu, David Schwarz, Hernan Stamati, Drew Bryant
Keywords: collision, conformation, crd, energy, pdb, secondary structure, steric, Van der Waals, VMD
Summary: This assigment introduces students to the visualization software VMD and allows them to get familiar with protein structures. Students are required to visualize protein conformations and understand the differences between structures based on their geometry. Students will rank the provided conformations based on their geometric differences.
Subject: Science and Technology
Language: English
Popularity: 78.92%
Revised: 2009-03-17
Revisions: 22
Assignment 2: Performing Rotations (m11624)
Maintainers: Lydia E. Kavraki, Amarda Shehu, David Schwarz, Hernan Stamati
Keywords: accumulating transformations, dihedral bond, homogenous transformation, Rotatable bond, rotation matrix, translation matrix
Summary: In this assignment students will manipulate protein structures through rotations of dihedral bonds. They will get a first-hand look at how rotation by dihedrals causes large scale motions in protein structures, and can cause steric clashes in a protein chain.
Subject: Science and Technology
Language: English
Popularity: 96.14%
Revised: 2007-04-10
Revisions: 6
Assignment 3: Inverse Kinematics (m11623)
Maintainers: Lydia E. Kavraki, Amarda Shehu, David Schwarz, Hernan Stamati
Subject: Science and Technology
Language: English
Popularity: 80.46%
Revised: 2007-03-20
Revisions: 7
Current Docking Research -- deprecated module (m11455)
Maintainers: Lydia E. Kavraki, David Schwarz, Amarda Shehu, Hernan Stamati
Subject: Science and Technology
Language: English
Popularity: 47.65%
Revised: 2006-05-09
Revisions: 11
Dimensionality Reduction Methods for Molecular Motion (m11461)
Maintainers: Lydia E. Kavraki, Amarda Shehu, David Schwarz, Hernan Stamati
Keywords: dimensionality reduction, Isomap, molecular motion, PCA, proteins
Summary: This module introduces concepts on dimensionality reduction, including Principal Components Analysis (PCA) and Isomap. It also shows how to apply them to molecular motion data, and how to interpret the resulting coordinates.
Subject: Science and Technology
Language: English
Popularity: 93.77%
Revised: 2007-06-11
Revisions: 10
Macromolecular Structure and Biomolecular Interactions -- deprecated module (m11612)
Maintainers: Lydia E. Kavraki, Amarda Shehu, David Schwarz, Hernan Stamati
Subject: Science and Technology
Language: Italiano
Popularity: 75.09%
Revised: 2006-05-09
Revisions: 6
Molecular Distance Measures (m11608)
Maintainers: Lydia E. Kavraki, Amarda Shehu, David Schwarz, Hernan Stamati, Brian Chen
Keywords: dRMSD, intramolecular distance, least RMSD, lRMSD, protein distance, RMSD, structure alignment
Summary: Given a set of structures of the same molecule, it is often necessary to decide which are more similar or less similar to each other. This module presents a few ways to approach that problem, including root mean squared distance (RMSD), least RMSD, and intramolecular distance measures.
Subject: Science and Technology
Language: English
Popularity: 92.84%
Revised: 2007-06-11
Revisions: 23
Molecular Shapes and Surfaces (m11616)
Maintainers: Lydia E. Kavraki, Amarda Shehu, David Schwarz, Hernan Stamati
Keywords: Alpha Shapes, Cavity, Delaunay Complex, Delaunay Triangulation, Molecule, Pocket, Point Set, Protein, Shape, Surface, Voronoi Diagrams
Summary: This module introduces students to a family of algorithms for assessing molecular shape, volume, surface area, and negative space (i.e., pockets and cavities).
Subject: Science and Technology
Language: English
Popularity: 91.25%
Revised: 2007-06-11
Revisions: 10
Motion Planning for Proteins: Biophysics and Applications (m11449)
Maintainers: Lydia E. Kavraki, Allison Heath, Amarda Shehu, David Schwarz, Hernan Stamati
Keywords: CHARMM, EST, force field, free energy, molecular potential, motion planning, path planner, planner, potential field, potential function, PRM, protein, robotics, RRT, SRS, tree-based
Summary: This module introduces the concept of free energy and potential fields in the context of protein conformation spaces and motion planning. It then provides examples of applications of motion planning techniques to problems from structural computational biology.
Subject: Science and Technology
Language: English
Popularity: 89.72%
Revised: 2007-03-22
Revisions: 20
[1] 2 Next 9 »
Popularity is measured as percentile rank of page views/day over all time
My Account
Repository
Total Collections: 1317
Total Modules: 21757