Index

Superpose Matched Residues...

Undo All

Undo Last

aligning

aligning sequences 1, 2

alpha carbon torsion convention

Amino Acid Residue tool

structure definition file

Quit

Amino Acid Selection tool

Keyboard

Non-standard

Undo Last

amino acids

analysis

Analyze Domain Structure

Analyze Domain Structure option

One Less Domain

One More Domain

Analyze Domain Structure tool

Analyze Secondary Structure

Reassign Residue Range

Reread MSF

Save to MSF

Undo Domain Edit

Write Domains to FIle

Write Geometry to FIle

Assign Secondary Structure

tools and options

Analyze Secondary Structure option

Alpha Carbon Atoms Only

Pick Residue

Pick Residue Range

Analyze Secondary Structure tool

Add Hydrogen Bonds

Calculate Hydrogen Bonds

Calculate Secondary Structure

Calculation Options

Color Options

Delete Hydrogen Bonds

Display Hydrogen Bonds

analyzing secondary structures

Applications menu

Protein Design

Apply Conformation option

Position folded fragment

axial vectors 1, 2

tilt angle/interaxial angle

B

building coordinates

BVALUE

C

Ca-Ca distance homology

scoring system

Calculate Accessibility

Color by Fraction Accessible

Calculate Accessibility option

Accessible Area...

Color Options

Contact Area

Calculate Accessibility tool

Atom Accessibility

Color by Atom

Color by Exception

Color by Side Chain

Excluded Zero Accessibility

calculating accessibility

List to Textport

Reread MSF

Residue Accessibility

Save to MSF

Write to File

calculating contact maps

close contacts

clustering algorithm

how calculated in QUANTA

commands

LIST ATOM

list location

modeler model_name

sys rm -rt directory_name

conservation profiles

contact area 1, 2

difference contact maps

difference plot

distance contact maps

energy contact maps

hydrogen bond interactions maps

interaction-type contact map

inter-residue Ca-Ca distances

inter-residue contacts

molecule display

plotting method

plotting secondary structure elements

residue type interaction maps

three major categories

three types of energy maps

contact plotting method

Create Homology Model

Create Homology Model tool

Change Unknown Structure

Copy

Copy Matched Residues

geometric structure definition file

CREBASE program 1, 2

D

data files

conversion

PHD format 1, 2

protein parameter file

sequence data format

database

creation

creation using the Search Fragment Database utility

database query 1, 2

databases

Align and Superpose Options

deleting residues

dendograms

definition in footnote

dialog

Alignment Weights

Calculate Accessible Area

Calculate Contact Area

Change Coloring Ranges

Change Displayed Map

Choose an Unknown Structure

Color Range

Color Secondary Structure

Contact Map 1, 2

Contact Map Color Ranges

Cutoff Difference in Average Distance

Database Search Parameters

Define Coloring Ranges

Define INTRA-template constraint

Define phi/psi Dihedrals

Define Protein Structure Database Query

Define Template

Define template name_search

Delete Template or Constraint

Display Overlay from Database Search

Display Selected Fragments

Enter Number of Domains

Fold Protein Main Chain

Fragment Display Mode

Fragment Modeling Options

Hydrophobic Profile Options

Match Option

Motif Superposition 1, 2

Protein Health Options

Protein Utilities Options

Score Parameters

Secondary Structure Analysis Parameters

Secondary Structure Title

Select Fragment to Display

Sequence Database

Side Chain Torsions

Specify Protein

Specify Proteins to Search

difference contact maps

E

Edit Protein

Amino Acid Selection

Edit Protein option

Regularization Options

Edit Protein tool

Change Terminal

Create MSF from Sequence

Delete

exclusion range of residues

Mutate

F

FASTA (.aa extension)

FASTA search algorithm overview

FASTA Sequence Searching

feature PDFs

file

$HYD_EXE/crebase

$HYD_EXE/msfgen

$HYD_LIB/database.dat 1, 2, 3

$HYD_LIB/motif.geo

$HYD_LIB/param.par

$HYD_LIB/pdbsequence.lib

$HYD_LIB/protein_param.dat

$HYD_LIB/protein_torsions.dat 1, 2, 3

$HYD_LIB/tmplat(noh/pol/all)/*.pdb

$HYD_LIB/wildcard.da

$HYD_LIB/wildcard.dat

$HYD_MSF/dmprep

$QNT_ROOT/ dmatrix/dmfile

$QNT_ROOT/db/crebase

$QNT_ROOT/db/crebase/crebase.inp

$QNT_ROOT/dmatrix/dmfile

dmfile

dmlist

HYD_LIB/harvard_torsion.dat

name_momany_predict.out

pdb_master.list 1, 2

pdbsequence.lib 1, 2, 3

wildcard.dat

file formats

Clustal

EMBL

FASTA

FASTA (.aa extension)

HAHU

NBRF-PIR (.pir extension)

QUANTA alignment

Swissprot

Swissprot (.sws extension)

folding residues

fragment searching

Bumps option

useful criteria for choosing a fragment

G

H

hbond convention

homology

copying

modeling 1, 2

homology (indicated)

homology, structural approaches

hydrogen addition

hydrogen bonds calculation

hydrophobic moments

hydrophobicity scales

I

inserting residues

interaction-type contact maps

inter-residue contacts

K

Kabsch and Sanders

Kabsch and Sanders formula

Kraulis, Per

L

Lee and Richards accessibility method

LIBRARY library_file

M

main chain conformation

matching residues

matching structure motifs

Model Backbone

Copy fold from another residue range

Model Backbone option

Accept Fragment

Carry connected residues

Display All Fragments

Display Next

Display Previous

Fold in regular structure

Fold to assigned secondary structure type

List Proteins

List Residues

Pick Alpha Carbon

Pick Alpha Carbon Range

Spin search side chain conformations

Undo All

Undo Last

User specified phi, psi and omega

with Bumps

Model Backbone tool

Apply Conformation

Build Coordinates

Harvard rotamer data file

Regularization Options

Regularize Region

Search Fragment Database

Model Side Chains

Model Side Chains option

Bump cutoff

Hydrogen Bond Cutoff

Protein torsion data file

Radius to display sphere

Spin Increment

Model Side Chains tool

Auto

modifying files to modify models

Reset

model_name.top 1, 2

model_name_dir/

model_name.B9999nn.pdb

MODELER

control file 1, 2

files

models

adding a disulfide bond

representing hydrogens

specifying run parameters

starting

Modeler

background theory

structure generation theory

MODELER (introduction)

$MODELER_ROOT/exec/ __defs.top.

modeling

modeling the protein backbone

modeling side chains

Motif Database

Motif Database option

Table Database Results

Motif Database tool

Save Structure to Database

Select Database

Select Overlay(s)

Show Overlays

motif log file keyword

LIBRARY library_file

MOLECULE msf_name

NMATCH number_of_matches

TEST molecule_name

mutating residues 1, 2

N

NBRF- PIR

NBRF-PIR (.pir extension)

NMATCH number_of_matches

O

optimization level

overview

FASTA search algorithm

P

palette

Accessibility

Align and Superpose

amino acid selection

Analyze Secondary Structure

Contact Maps

Create Homology Model

Predict Secondary Structure

Profile Analysis

Protein Database

Superpose Folding

PDB

retrieving textual information with Protein Information utility

searching for close sequences

plotting secondary structure elements

positioning the fold fragment

PostScript

Predict Secondary Structure

Predict Secondary Structure tool

Edit Secondary Structure

Plot Conservation Profile

Plot GOR Prediction

Plot Holley/Karplus Prediction

Plot Hydrophobic Profile

Plot Momany Prediction

Profile Options

Read from MSF

Save to MSF

probability density functions

basis and feature

for bond lengths, bond angles and dihedrals

observed in known protein structures

Profile Analysis

Profile Analysis tool

Align

Dot Plot

Plot Sequence Profile

Plot Structure Profile

profiles

program

$HYD_EXE/search job_name

Protein Design

Protein Design Alignment palette

Protein Design palette

protein domains

importance of the cutoff distance

loop regions

protein geometry

Protein Health

analysis of multiple conformations

Dunbrack and Karplus rotamer definitions

exception mnemonics

presenting the results of the health check

Dunbrack and Karplus Rotamer Library

uses

Protein Health library

Protein Health option

Highlights

Phi/psi Options

Protein Health tool

Buried Hydrophilic and Exposed Hydrophobic Residues

Buried Polar Atoms

Chirality

Close Contacts

Convert PDB files to CSR

Display Conformation

Display Exceptions

Holes

List Exceptions to Textport

List Phi/psi to Textport

Main Chain Conformation

Tabulate MultiConformations

Phi/Psi Plots

Select Active Residues

Side chain conformation

Undefined Coordinates

Write Exceptions to File

Write Phi/psi to File

protein homology modeling

Protein Information

running a query

Maximum crystal resolution

Protein Information tool

Output log file name

Position in database between structure number

Search for keyword or PDB

protein modeling

protein sequence library

pdbsequence.lib file

Protein Utilities

Color By Sequence Properties

Protein Utilities option

Color by Homology

Color by Structure Properties

profile/sequence comparison

Protein Utilities palette 1, 2

Protein Utilities tool

Center

Legend

proteins

modeling the backbone

profile comparison

profiles

simple representations

R

reference motif

regularization 1, 2

when to use regularization

regularizing regions

residues

accessibility homology

accessibility scoring

environment

mutating, inserting, and deleting

rotamers

restraining dihedral angles 1, 2

restraints

Retrieving Protein Information

RMS Deviation tool

rotamer conformations

c1 and c2 dihedrals

rotamer libraries

Rotamer Library Types

rotamers

Run Modeler

S

scoring

scoring schemes

search command

ATOL

CONS

CTOL

DBAS

DBUG

DIST

DTOL

INFO

MKEY

MNAM

MRNG

NHIT

RESD

RSLN

SIDE

STOL

TMPL

WILD

search commands

Search Fragment Database tool

Holley/Karplus prediction

searching

running a search

the structure database

secondary structure

analyzing

assignment

3-turn

4-turn

5-turn

alpha helix

beta bulges

beta strand

extended conformation

folded conformation

GOR prediction

homology

homology scoring system

segments

sequence alignment 1, 2

Sequence Database

FASTA program

Change sequence database file

Sequence Database tool

Enter search sequence

Read sequence search log file

Read Sequence Data File 1, 2

Read Sequence/Alignment File

Residue IDs and names

Selecting the viewing area

Sequence Viewer icon

Expand

Focus

G Toggle Graph Display

sequences

data

saving sequences and alignment between sessions

side chain conformation restraints

side chains

automatic modeling

bump cut-off distance

solvent accessibility

coloring schemes

solvent accessible surface area

solvent sphere

calculating the solvent surface

Structural Database

Structural Database option

Define INTRA-template constraint

Define template

Define template name_search

Using Distance Constraints

Using Residue Separation Constraints.

Write to default MSF name

Structural Database query

browsing database search results

Structural Database tool

Define constraint between two templates

Define Query

Display All Fragments

Display Next

Display Option

Display Previous

List secondary structure and amino acid wildcards

List/delete existing template(s) and constraint(s)

Read Hit Fragments

Read in database search results

Select extra neighboring residues to be displayed

Select hits to display

Specify proteins to search

Superpose Fragments

structure superposition

Superpose Folding Motif

calculated from axial vectors

superpose folding motifs

Superpose Motif

demonstration

Geometric Criteria of Secondary Structures

Superpose Motif option

Individual Secondary Structure

Motif Tables

Number of matched elements

Superposition RMS difference

Undo Alignment

Superpose Motif tool

Align Sequence

All Overlays

Change Activity Tools

Clear Display