- nnPredict:
A neural network method (Cohen et al., UCSF)
nnPredict:
Input Form
BMERC
PSA (Protein Sequence Analysis)
- Probabilistic discrete state space method (smoothing and
filtering functions)
- BMERC
PSA: input form
C. Methods using multiple sequence alignments
- DSC:
Discrimination of Protein Secondary Structure
Class
(King
& Sternberg)
- The method is based on the GOR approach and mean moment of
hydrophobicity.
Linear discrimination method is used for the final prediction. Original
DSC currently
unavailable; Program 'Prof' or 'Son of DSC' can be accessed at the
following link:
Prof:
Input form
- PREDATOR:
Frischman & Argos (EMBL): Info page
- Propensity of secondary stgructure, hydrogen bonded residues,
pair-wise
alignment
- The
PredictProtein Home Page: Rost, B: Columbia University
"You submit any protein sequence. PredictProtein retrieves similar
sequences in the database
and predicts aspects of protein structure"
The
PredictProtein: input form
- MASIA:
Home page
- "Multiple Sequence Alignment Investigation and Analysis",
developed in
W.Braun's group
- MASIA
:Input form
Search for Other Structural
Features
- COILS:
to predict coiled-coil structures
- PROSITE
database of protein families and domains
Domain identification
Pfam:
Protein families database of alignments and HMMs
Search
Pfam
Material
on Hidden Markov Models (UC Santa Cruz)
The
ProDom protein domain database: Home page and starting point for
searches
A compilation of homologous domains, searcheable in different ways
ICGEB: International Centre
for
Genetic Engineering & Biotechnology, Trieste, Italy
The
SBASE 7.0 Protein domain library and search tools
Protein Fold Recognition/ Threading
- SCOP:
Structural Classification of Proteins
- "structural and evolutionay relationships between all
proteins
whose
structure is known".
- Can be accessed in four of different ways starting from the above
link.
3D-PSSM
web server, Biomolecular Modelling Laboratory, Imperial Cancer Research
Fund, London
"A fast web-based method for Protein Fold Recognition using 1D and
3D Sequence
Profiles coupled with Secondary Structure and Solvation Potential
Information"
Bioinbgu,
Bioinformatics
server at Ben Gurion University, Israel 0
-
- GenThreader,
from PSIpred, Protein Bioinformatics Group, Department of Biological
Sciences,
University of Warwick
- PSIpred
Input form
-
- TOPITS,
PredictProtein server @ Columbia University
Threading a sequence
through a set of structures: 123D+ Homepage
123D+
input form
FFAS
Karplus
1 & 2
Karplus
3
Homology Modeling (Comparative Modeling)
- Swiss-Model
Home page
- WHAT
IF interface at EMBL, Heidelberg
Ab initio Protein Modeling
CASP: Protein
structure
prediction center- MASIA
- Multiple Aligned
Protein Structure Analysis and Validation
- PROCHECK
Home page: How to download, install, and run the program
To check the stereochemical quality of a protein structure
- WHAT
IF: Home page
A general protein structure analysis program.
WHAT_CHECK:
protein structure verification tools from WHAT IF
SCSBMB Software Links
PCPMer:
A set of Physical Chemical Property
based Motif Analyzer tools
InterProSurf: Tool for prediction of
functional sites in protein monomer surfaces
- GETAREA:
Program
developed in our group to calculate Solvent Accessible Surface Areas,
Atomic
Solvation Energies,
- and their Gradients for macromolecules.