MODELLER A Program for Protein Structure Modeling Release 7v7 Andrej Saliˇ with help from Ben Webb, M.S. Madhusudhan, Min-Yi Shen, Marc A. Martı-Renom, Narayanan Eswar, Frank Alber, Baldomero Oliva, Andr´as Fiser, Roberto S´anchez, Bozidar Yerkovich, Azat Badretdinov, Francisco Melo, John P. Overington, and Eric Feyfant email [email protected] URL http://salilab.org/modeller/ September 2004 ii Contents Copyright notice xiii Acknowledgments xv 1 Introduction 1 1.1 What is Modeller? . 1 1.2 Modeller bibliography . 2 1.3 Distribution . 3 1.4 Installation . 4 1.5 Bug reports . 7 1.6 Method for comparative protein structure modeling by Modeller . 8 1.7 Tutorial on using Modeller for comparative modeling . 10 1.7.1 Preparing input files . 10 1.7.2 Running Modeller . 11 1.7.3 Automated alignment and comparative modeling . 11 1.8 Frequently asked questions (FAQ) and examples . 13 1.9 Modeller updates . 24 1.9.1 Changes since release 6v2 . 24 1.9.2 Changes between releases 4 and 6v2 . 24 2 Modeller commands 27 2.1 Miscellaneous rules and features of Modeller . 27 2.1.1 Modeller system . 27 2.1.2 Running Modeller scripts . 27 2.1.3 Controlling breakpoints and the amount of output . 28 2.1.4 File naming . 28 2.1.5 File types . 30 2.1.6 Format of the command description . 30 2.2 Stereochemical parameters and molecular topology . 32 2.2.1 Modeling residues with non-existing or incomplete entries in the topology and parameter libraries . 32 2.2.2 READ RESTYP LIB | read residue type library . 33 2.2.3 READ TOPOLOGY | read residue topology library . 33 2.2.4 READ PARAMETERS | read parameters library . 34 2.2.5 READ ATOM CLASSES | read classification of atom types . 34 iii iv CONTENTS 2.2.6 GENERATE TOPOLOGY | generate MODEL topology . 34 2.2.7 PATCH | patch MODEL topology . 35 2.2.8 PATCH SS TEMPLATES | guess MODEL disulfides from templates . 36 2.2.9 PATCH SS MODEL | guess MODEL disulfides from model structure . 38 2.2.10 MUTATE MODEL | mutate selected MODEL residues . 38 2.2.11 MAKE TOPOLOGY MODEL | make a subset topology library . 39 2.2.12 WRITE TOPOLOGY MODEL | write residue topology library . 40 2.3 Handling of atomic coordinates . 41 2.3.1 READ MODEL | read coordinates for MODEL . 41 2.3.2 READ MODEL2 | read coordinates for MODEL2 . 41 2.3.3 WRITE MODEL | write MODEL . 42 2.3.4 WRITE MODEL2 | write MODEL2 . 42 2.3.5 BUILD MODEL | build MODEL coordinates from topology . 43 2.3.6 UNBUILD MODEL | undefine MODEL coordinates . 44 2.3.7 TRANSFER XYZ | copy templates' coordinates to MODEL . 44 2.3.8 TRANSFER RES NUMB | residue numbers from MODEL2 to MODEL . 46 2.3.9 RENAME SEGMENTS | rename MODEL segments . 47 2.3.10 PICK ATOMS | select atoms in MODEL . 47 2.3.11 PICK HOT ATOMS | pick atoms violating restraints . 50 2.3.12 RANDOMIZE XYZ | randomize MODEL coordinates . 51 2.3.13 IUPAC MODEL | standardize certain dihedral angles . 52 2.3.14 REORDER ATOMS | standardize order of MODEL atoms . 52 2.3.15 ROTATE DIHEDRALS | change dihedral angles . 53 2.3.16 ORIENT MODEL | center and orient MODEL . 54 2.3.17 ROTATE MODEL | rotate and translate MODEL . 54 2.3.18 WRITE DATA | write derivative MODEL data . 55 2.3.19 WRITE PDB XREF | write residue number/index correspondence . 57 2.3.20 MAKE REGION | define a random surface patch of atoms . 58 2.4 Comparison and searching of sequences and structures . 60 2.4.1 Alignment file format . 60 2.4.2 READ ALIGNMENT | read sequences and/or their alignment . 62 2.4.3 READ ALIGNMENT2 | read 2nd alignment . 63 2.4.4 CHECK ALIGNMENT | check alignment for modeling . 64 2.4.5 COLOR ALN MODEL | color MODEL according to alignment . 64 2.4.6 COMPARE ALIGNMENTS | compare two alignments . 65 2.4.7 SEQUENCE TO ALI | copy MODEL sequence and coordinates to alignment . 66 2.4.8 WRITE ALIGNMENT | write sequences and/or their alignment . 67 2.4.9 EDIT ALIGNMENT | edit overhangs in alignment . 68 2.4.10 DESCRIBE | describe proteins . 69 2.4.11 ID TABLE | calculate percentage sequence identities . 69 2.4.12 SEQUENCE COMPARISON | compare sequences in alignment . 70 2.4.13 DENDROGRAM | clustering . 71 2.4.14 PRINCIPAL COMPONENTS | clustering . 71 CONTENTS v 2.4.15 ALIGN | align two (blocks of) sequences . 71 2.4.16 ALIGN2D | align sequences with structures . 73 2.4.17 MALIGN | align two or more sequences . 75 2.4.18 ALIGN CONSENSUS | consensus sequence alignment . 76 2.4.19 SUPERPOSE | superpose MODEL2 on MODEL given alignment . 77 2.4.20 COMPARE | compare 3D structures given alignment . 80 2.4.21 ALIGN3D | align two structures . 81 2.4.22 MALIGN3D | align two or more structures . 82 2.4.23 ALN TO PROF | convert alignment to profile format . 84 2.4.24 PROF TO ALN | profile to alignment . 85 2.4.25 READ PROFILE | read a profile of a sequence . 85 2.4.26 WRITE PROFILE | write a profile . 87 2.4.27 BUILD PROFILE | Build a profile for a given sequence or alignment . 87 2.4.28 READ SEQUENCE DB | read a database of sequences . 90 2.4.29 WRITE SEQUENCE DB | write a database of sequences . 90 2.4.30 EXPAND ALIGNMENT | put all models into alignment . 91 2.4.31 SEQUENCE SEARCH | search for similar sequences . 91 2.4.32 SEQFILTER | cluster sequences by sequence-identity . 93 2.4.33 DELETE ALIGNMENT | delete alignment . 95 2.4.34 SEGMENT MATCHING | align segments . 95 2.5 Calculation of spatial restraints . 97 2.5.1 Specification of restraints . 97 2.5.2 Specification of pseudo atoms . 98 2.5.3 MAKE RESTRAINTS | make restraints . 103 2.5.4 DEFINE SYMMETRY | define similar segments . 107 2.5.5 PICK RESTRAINTS | pick restraints for selected atoms . 109 2.5.6 CONDENSE RESTRAINTS | remove unselected restraints . 110 2.5.7 ADD RESTRAINT | add restraint . 111 2.5.8 DELETE RESTRAINT | unselect restraint . 112 2.5.9 REINDEX RESTRAINTS | renumber MODEL2 restraints for MODEL . 112 2.5.10 SPLINE RESTRAINTS | approximate restraints by splines . 113 2.5.11 READ RESTRAINTS | read spatial restraints . ..