doc/apps/public/antibody/antibody.dox File Reference

Variables
Checkout trunk antibody Change antibody scripts rampaths txt to set the paths to match your directory structure Copy the following files to directory where simulation will be	run
Checkout trunk antibody Change antibody scripts rampaths txt to set the paths to match your directory structure Copy the following files to directory where simulation will be more details are provided in ram_blankcdrs pl Change the hardcoded paths in the following file to match your directory	structure
Checkout trunk antibody Change antibody scripts rampaths txt to set the paths to match your directory structure Copy the following files to directory where simulation will be more details are provided in ram_blankcdrs pl Change the hardcoded paths in the following file to match your directory which already	contains
Checkout trunk antibody Change antibody scripts rampaths txt to set the paths to match your directory structure Copy the following files to directory where simulation will be more details are provided in ram_blankcdrs pl Change the hardcoded paths in the following file to match your directory which already Kayode A	Sanni
Checkout trunk antibody Change antibody scripts rampaths txt to set the paths to match your directory structure Copy the following files to directory where simulation will be more details are provided in ram_blankcdrs pl Change the hardcoded paths in the following file to match your directory which already Kayode A Jiye Shi &Jeffrey J	Gray
Checkout trunk antibody Change antibody scripts rampaths txt to set the paths to match your directory structure Copy the following files to directory where simulation will be more details are provided in ram_blankcdrs pl Change the hardcoded paths in the following file to match your directory which already Kayode A Jiye Shi &Jeffrey J Analysis and Modeling of the Variable Region of Camelid Single Domain	Antibodies
Checkout trunk antibody Change antibody scripts rampaths txt to set the paths to match your directory structure Copy the following files to directory where simulation will be more details are provided in ram_blankcdrs pl Change the hardcoded paths in the following file to match your directory which already Kayode A Jiye Shi &Jeffrey J Analysis and Modeling of the Variable Region of Camelid Single Domain J	Immunology
Checkout trunk antibody Change antibody scripts rampaths txt to set the paths to match your directory structure Copy the following files to directory where simulation will be more details are provided in ram_blankcdrs pl Change the hardcoded paths in the following file to match your directory which already Kayode A Jiye Shi &Jeffrey J Analysis and Modeling of the Variable Region of Camelid Single Domain J For classical Fv	modeling
Checkout trunk antibody Change antibody scripts rampaths txt to set the paths to match your directory structure Copy the following files to directory where simulation will be more details are provided in ram_blankcdrs pl Change the hardcoded paths in the following file to match your directory which already Kayode A Jiye Shi &Jeffrey J Analysis and Modeling of the Variable Region of Camelid Single Domain J For classical Fv Aroop Sircar Sidhartha Chaudhury &Jeffrey J Toward high resolution homology modeling of antibody Fv regions and application to antibody antigen	docking
Checkout trunk antibody Change antibody scripts rampaths txt to set the paths to match your directory structure Copy the following files to directory where simulation will be more details are provided in ram_blankcdrs pl Change the hardcoded paths in the following file to match your directory which already Kayode A Jiye Shi &Jeffrey J Analysis and Modeling of the Variable Region of Camelid Single Domain J For classical Fv Aroop Sircar Sidhartha Chaudhury &Jeffrey J Toward high resolution homology modeling of antibody Fv regions and application to antibody antigen	Proteins
Checkout trunk antibody Change antibody scripts rampaths txt to set the paths to match your directory structure Copy the following files to directory where simulation will be more details are provided in ram_blankcdrs pl Change the hardcoded paths in the following file to match your directory which already Kayode A Jiye Shi &Jeffrey J Analysis and Modeling of the Variable Region of Camelid Single Domain J For classical Fv Aroop Sircar Sidhartha Chaudhury &Jeffrey J Toward high resolution homology modeling of antibody Fv regions and application to antibody antigen Function and	Bioinformatics

Variable Documentation

Checkout trunk antibody Change antibody scripts rampaths txt to set the paths to match your directory structure Copy the following files to directory where simulation will be more details are provided in ram_blankcdrs pl Change the hardcoded paths in the following file to match your directory which already Kayode A Jiye Shi& Jeffrey J Analysis and Modeling of the Variable Region of Camelid Single Domain Antibodies

Checkout trunk antibody Change antibody scripts rampaths txt to set the paths to match your directory structure Copy the following files to directory where simulation will be more details are provided in ram_blankcdrs pl Change the hardcoded paths in the following file to match your directory which already Kayode A Jiye Shi& Jeffrey J Analysis and Modeling of the Variable Region of Camelid Single Domain J For classical Fv Aroop Sircar Sidhartha Chaudhury& Jeffrey J Toward high resolution homology modeling of antibody Fv regions and application to antibody antigen Function and Bioinformatics

Checkout trunk antibody Change antibody scripts rampaths txt to set the paths to match your directory structure Copy the following files to directory where simulation will be more details are provided in ram_blankcdrs pl Change the hardcoded paths in the following file to match your directory which already contains

Referenced by protocols::forge::build::SegmentRebuild::modify_impl(), protocols::match::BumpGrid::occupied(), core::scoring::dssp::StrandPairing::paired(), and protocols::features::BetaTurnDetectionFeatures::validate_ramachandran_hash().

Checkout trunk antibody Change antibody scripts rampaths txt to set the paths to match your directory structure Copy the following files to directory where simulation will be more details are provided in ram_blankcdrs pl Change the hardcoded paths in the following file to match your directory which already Kayode A Jiye Shi& Jeffrey J Analysis and Modeling of the Variable Region of Camelid Single Domain J For classical Fv Aroop Sircar Sidhartha Chaudhury& Jeffrey J Toward high resolution homology modeling of antibody Fv regions and application to antibody antigen docking

Referenced by protocols::hybridization::DomainAssembly::apply(), protocols::surface_docking::FullatomRelaxMover::apply(), protocols::ub_e2c::ubi_e2c_modeler::centroid_mode_perturbation(), protocols::ub_e2c::ubi_e2c_modeler::init_k48r_perturbation(), protocols::ub_e2c::ubi_e2c_modeler::initial_perturbation(), protocols::ub_e2c::ubi_e2c_modeler::monoub_centroid_mode_perturbation(), protocols::ub_e2c::ubi_e2c_modeler::monoub_first_perturbation(), protocols::ub_e2c::ubi_e2c_modeler::monoub_initial_perturbation(), protocols::ub_e2c::ubi_e2c_modeler::optimize_cov_bond(), protocols::hybridization::DomainAssembly::run(), protocols::docking::DockMinMover::set_default(), and protocols::docking::DockMCMCycle::set_default().

Checkout trunk antibody Change antibody scripts rampaths txt to set the paths to match your directory structure Copy the following files to directory where simulation will be more details are provided in ram_blankcdrs pl Change the hardcoded paths in the following file to match your directory which already Kayode A Jiye Shi &Jeffrey J Analysis and Modeling of the Variable Region of Camelid Single Domain J For classical Fv Aroop Sircar Sidhartha Chaudhury &Jeffrey J Gray

Checkout trunk antibody Change antibody scripts rampaths txt to set the paths to match your directory structure Copy the following files to directory where simulation will be more details are provided in ram_blankcdrs pl Change the hardcoded paths in the following file to match your directory which already Kayode A Jiye Shi& Jeffrey J Analysis and Modeling of the Variable Region of Camelid Single Domain J Immunology

Checkout trunk antibody Change antibody scripts rampaths txt to set the paths to match your directory structure Copy the following files to directory where simulation will be more details are provided in ram_blankcdrs pl Change the hardcoded paths in the following file to match your directory which already Kayode A Jiye Shi& Jeffrey J Analysis and Modeling of the Variable Region of Camelid Single Domain J For classical Fv modeling

Checkout trunk antibody Change antibody scripts rampaths txt to set the paths to match your directory structure Copy the following files to directory where simulation will be more details are provided in ram_blankcdrs pl Change the hardcoded paths in the following file to match your directory which already Kayode A Jiye Shi& Jeffrey J Analysis and Modeling of the Variable Region of Camelid Single Domain J For classical Fv Aroop Sircar Sidhartha Chaudhury& Jeffrey J Toward high resolution homology modeling of antibody Fv regions and application to antibody antigen Proteins

Checkout trunk antibody Change antibody scripts rampaths txt to set the paths to match your directory structure Copy the following files to directory where simulation will be run

Referenced by core::pack::pack_rotamers_loop().

Checkout trunk antibody Change antibody scripts rampaths txt to set the paths to match your directory structure Copy the following files to directory where simulation will be more details are provided in ram_blankcdrs pl Change the hardcoded paths in the following file to match your directory which already Kayode A Sanni

Checkout trunk antibody Change antibody scripts rampaths txt to set the paths to match your directory structure Copy the following files to directory where simulation will be more details are provided in ram_blankcdrs pl Change the hardcoded paths in the following file to match your directory structure

Referenced by protocols::loophash::LoopHashMoverWrapper::apply(), and protocols::optimize_weights::IterativeOptEDriver::make_simple_ssd_from_pdb().