Contents

• List of Figures
• List of Tables
• Introduction
  • What is MODELLER?
  • MODELLER bibliography
  • Distribution
  • Installation
  • Bug reports
  • Method for comparative protein structure modeling by MODELLER
  • Comparative protein modeling primer
    • Finding structures and sequences related to the target sequence
    • Preparing an initial family alignment of all structures and sequences
    • Becoming familiar with the family fold and improving the alignment
    • Selecting the templates
    • Model building
    • Evaluating the models
    • Repeat the cycle
  • Tutorial on using MODELLER for comparative modeling
    • Preparing input files
    • Running MODELLER
    • Fully automated comparative modeling
    • Improved modeling of loops in MODELLER-6
  • Frequently asked questions (FAQ) and examples
  • MODELLER updates
    • Major changes in Releases 5 and 6
    • Detailed chronological listing of some changes since MODELLER-4 release on 17 June, 1997
  
  
• MODELLER commands
  • Miscellaneous rules and features of MODELLER
    • MODELLER system
    • Running MODELLER scripts
    • Controlling breakpoints and the amount of output
    • File naming
    • File types
    • Format of the command description
  • Stereochemical parameters and molecular topology
    • Modeling residues with non-existing or incomplete entries in the topology and parameter libraries
    • READ_RESTYP_LIB -- read residue type library
    • READ_TOPOLOGY -- read residue topology library
    • READ_PARAMETERS -- read parameters library
    • READ_ATOM_CLASS -- read classification of atom types
    • GENERATE_TOPOLOGY -- generate MODEL topology
    • PATCH -- patch MODEL topology
    • PATCH_SS_TEMPLATES -- guess MODEL disulfides from templates
    • PATCH_SS_MODEL -- guess MODEL disulfides from model structure
    • MUTATE_MODEL -- mutate selected MODEL residues
    • MAKE_TOPOLOGY_MODEL -- make a subset topology library
    • WRITE_TOPOLOGY_MODEL -- write residue topology library
  • Handling of atomic coordinates
    • READ_MODEL -- read coordinates for MODEL
    • READ_MODEL2 -- read coordinates for MODEL2
    • WRITE_MODEL -- write MODEL
    • WRITE_MODEL2 -- write MODEL2
    • BUILD_MODEL -- build MODEL coordinates from topology
    • TRANSFER_XYZ -- copy templates' coordinates to MODEL
    • TRANSFER_RES_NUMB -- residue numbers from MODEL2 to MODEL
    • RENAME_SEGMENTS -- rename MODEL segments
    • PICK_ATOMS -- select atoms in MODEL
    • PICK_HOT_ATOMS -- pick atoms violating restraints
    • RANDOMIZE_XYZ -- randomize MODEL coordinates
    • IUPAC_MODEL -- standardize certain dihedral angles
    • REORDER_ATOMS -- standardize order of MODEL atoms
    • ROTATE_DIHEDRALS -- change dihedral angles
    • ORIENT_MODEL -- center and orient MODEL
    • ROTATE_MODEL -- rotate and translate MODEL
    • WRITE_DATA -- write derivative MODEL data
    • WRITE_PDB_XREF -- write residue topology library
    • MAKE_REGION -- define a random surface patch of atoms
  • Comparison and searching of sequences and structures
    • Alignment file format
    • READ_ALIGNMENT -- read sequences and/or their alignment
    • READ_ALIGNMENT2 -- read 2nd alignment
    • CHECK_ALIGNMENT -- check alignment for modeling
    • COLOR_ALN_MODEL -- color MODEL according to alignment
    • COMPARE_ALIGNMENTS -- compare two alignments
    • SEQUENCE_TO_ALI -- copy MODEL sequence and coordinates to alignment
    • WRITE_ALIGNMENT -- write sequences and/or their alignment
    • DESCRIBE -- describe proteins
    • ID_TABLE -- calculate percentage sequence identities
    • SEQUENCE_COMPARISON -- compare sequences in alignment
    • DENDROGRAM -- clustering
    • PRINCIPAL_COMPONENTS -- clustering
    • ALIGN -- align two (blocks of) sequences
    • ALIGN2D -- align sequences with structures
    • MALIGN -- align two or more sequences
    • ALIGN_CONSENSUS -- consensus sequence alignment
    • SUPERPOSE -- superpose MODEL2 on MODEL given alignment
    • COMPARE -- compare 3D structures given alignment
    • ALIGN3D -- align two structures
    • MALIGN3D -- align two or more structures
    • EXPAND_ALIGNMENT -- put all models into alignment
    • SEQUENCE_SEARCH -- search for similar sequences
    • DELETE_ALIGNMENT -- delete alignment
    • SEGMENT_MATCHING -- align segments
  • Calculation of spatial restraints
    • Specification of restraints
    • Specification of pseudo atoms
    • MAKE_RESTRAINTS -- make restraints
    • DEFINE_SYMMETRY -- define similar segments
    • PICK_RESTRAINTS -- pick restraints for selected atoms
    • CONDENSE_RESTRAINTS -- remove unselected restraints
    • ADD_RESTRAINT -- add restraint
    • DELETE_RESTRAINT -- unselect restraint
    • REINDEX_RESTRAINTS -- renumber MODEL2 restraints for MODEL
    • SPLINE_RESTRAINTS -- approximate restraints by splines
    • READ_RESTRAINTS -- read spatial restraints
    • WRITE_RESTRAINTS -- write spatial restraints
  • Optimization of the model
    • MAKE_SCHEDULE -- create optimization schedule
    • READ_SCHEDULE -- read optimization schedule
    • WRITE_SCHEDULE -- write optimization schedule
    • ENERGY -- evaluate MODEL given restraints
    • OPTIMIZE -- optimize MODEL given restraints
    • SWITCH_TRACE -- open new optimization trace file
    • DEBUG_FUNCTION -- test code self-consistency
  
  
• MODELLER scripts
  • Flowchart of comparative modeling by MODELLER
  • Script for comparative modeling
  • Script for modeling of loops
  
  
• TOP, MODELLER scripting language
  • The source file
  • TOP Commands
    • DEFINE_INTEGER -- define integer variables
    • DEFINE_LOGICAL -- define logical variables
    • DEFINE_REAL -- define real variables
    • DEFINE_STRING -- define string variables
    • SET -- set variable
    • OPERATE -- perform mathematic operation
    • STRING_OPERATE -- perform string operation
    • RESET -- reset TOP
    • OPEN -- open input file
    • WRITE -- write TOP objects
    • READ -- read record from input file
    • CLOSE -- close an input file
    • WRITE_TOP -- write the TOP program
    • SYSTEM -- execute system command
    • INQUIRE -- check if file exists
    • GO_TO -- jump to label
    • LABEL -- place jump label
    • INCLUDE -- include TOP file
    • CALL -- call TOP subroutine
    • SUBROUTINE -- define TOP subroutine
    • RETURN -- return from TOP subroutine
    • END_SUBROUTINE -- end definition of TOP subroutine
    • DO -- DO loop
    • IF -- conditional statement for numbers
    • STRING_IF -- conditional statement for strings
    • STOP -- exit TOP
  • Predefined TOP variables
  
  
• Methods
  • Dynamic programming for sequence and structure comparison and searching
    • Pairwise comparison
    • Variable gap penalty
    • Local versus global alignment
    • Similarity versus distance scores
    • Multiple comparisons
  • Optimization of the objective function by MODELLER
    • Function
    • Optimizers
  • Equations used in the derivation of the molecular pdf
    • Features and their derivatives
    • Restraints and their derivatives
  • List of commands, arguments, and default values
  
  
• Bibliography
• Index