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The Magnesium Project

Volunteer Resources - Modeling Systems & Chemical Reactions

IPRS, Inc.

Software/Computer Tools

For the latest updates one might use AI/ML tools like Google's Bard, ChatGPT, et al.
Cn3D – 3D structure visualization
rasMOL – molecular modeling and visualization
SMILES – chemical naming system
FoldIt – protein folding modeling software
AlphaFold - protein structure prediction - see recent enhancements and "competition"
PIDD - Protein Inter-Atomic Distance Differences -  at
Proteopedia wiki – see also

 Structural analysis





Swiss-Model (via ExPASy)

            Pharmaceutical Compounds / Ligands / Agonists / Antagonists, etc. –IUPHAR

            BLAST and BLASTP – NIH

The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

      Compare multiple sequences using 
            Dotlet  at


 Models / Tools

            GESAPI – Modeling language

            SBML – Systems Biology Markup Language – developed at Caltech, et al.


Miscellaneous proprietary tools/modeling software – Comsol – etc.

Chemical Databases

American Chemical Society – have to pay to get full articles, but can get abstracts and citations and go to a library to copy the full article.

            Pharmaceutical Compounds / Ligands / Agonists / Antagonists, etc. – IUPHAR

Protein Analysis Tools

Topology prediction

·         PSORT - Prediction of protein subcellular localization

·         TargetP - Prediction of subcellular location

·         DAS - Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method (Stockholm University)

·         HMMTOP - Prediction of transmembrane helices and topology of proteins (Hungarian Academy of Sciences)

·         PredictProtein - Prediction of transmembrane helix location and topology (Columbia University)

·         SOSUI - Prediction of transmembrane regions (TUAT; Tokyo Univ. of Agriculture & Technology)

·         TMAP - Transmembrane detection based on multiple sequence alignment (Karolinska Institut; Sweden)

·         TMHMM - Prediction of transmembrane helices in proteins (CBS; Denmark)

·         TMpred - Prediction of transmembrane regions and protein orientation (EMBnet-CH)

·         TopPred 2 - Topology prediction of membrane proteins (Stockholm University)


Primary structure analysis

·         ProtParam - Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, pI, extinction coefficient, etc.)

·         Compute pI/Mw - Compute the theoretical pI and Mw from a Swiss-Prot or TrEMBL entry or for a user sequence

·         MW, pI, Titration curve - Computes pI, composition and allows to see a titration curve

·         REP - Searches a protein sequence for repeats

·         REPRO - De novo repeat detection in protein sequences

·         Radar - De novo repeat detection in protein sequences

·         SAPS - Statistical analysis of protein sequences at EMBnet-CH [Also available at EBI]

·         Coils - Prediction of coiled coil regions in proteins (Lupas's method) at EMBnet-CH [Also available at PBIL]

·         Paircoil - Prediction of coiled coil regions in proteins (Berger's method)

·         Multicoil - Prediction of two- and three-stranded coiled coils

·         2ZIP - Prediction of Leucine Zippers

·         PESTfind - Identification of PEST regions at EMBnet Austria

·         HLA_Bind - Prediction of MHC type I (HLA) peptide binding

·         SYFPEITHI - Prediction of MHC type I and II peptide binding

·         ProtScale Amino acid scale representation (Hydrophobicity, other conformational parameters, etc.)

·         Drawhca - Draw an HCA (Hydrophobic Cluster Analysis) plot of a protein sequence

·         Protein Colourer - Tool for coloring your amino acid sequence

·         Three To One - Tool to convert a three-letter coded amino acid sequence to single letter code

·         Colorseq - Tool to highlight (in red) a selected set of residues in a protein sequence

·         HelixWheel / HelixDraw - Representations of a protein fragment as a helical wheel

·         RandSeq - Random protein sequence generator


Secondary structure prediction

·         AGADIR - An algorithm to predict the helical content of peptides

·         APSSP - Advanced Protein Secondary Structure Prediction Server

·         GOR - Garnier et al, 1996

·         HNN - Hierarchical Neural Network method (Guermeur, 1997)

·         Jpred - A consensus method for protein secondary structure prediction at University of Dundee

·         JUFO - Protein secondary structure prediction from sequence (neural network)

·         nnPredict - University of California at San Francisco (UCSF)

·         PredictProtein - PHDsec, PHDacc, PHDhtm, PHDtopology, PHDthreader, MaxHom, EvalSec from Columbia University

·         Prof - Cascaded Multiple Classifiers for Secondary Structure Prediction

·         PSA - BioMolecular Engineering Research Center (BMERC) / Boston

·         PSIpred - Various protein structure prediction methods at Brunel University

·         SOPMA - Geourjon and Delιage, 1995

·         SSpro - Secondary structure prediction using bidirectional recurrent neural networks at University of California


Tertiary structure

Tertiary structure analysis

·         iMolTalk - An Interactive Protein Structure Analysis Server

·         MolTalk - A computational environment for structural bioinformatics

·         Seq2Struct - A web resource for the identification of sequence-structure links

Tertiary structure prediction

Comparative modeling

·         SWISS-MODEL An automated knowledge-based protein modelling server

·         3Djigsaw - Three-dimensional models for proteins based on homologues of known structure

·         CPHmodels - Automated neural-network based protein modelling server

·         ESyPred3D - Automated homology modeling program using neural networks

·         Geno3d - Automatic modelling of protein three-dimensional structure

·         SDSC1 - Protein Structure Homology Modeling Server


·         3D-PSSM - Protein fold recognition using 1D and 3D sequence profiles coupled with secondary structure information (Foldfit)

·         Fugue - Sequence-structure homology recognition

·         Libellula - Neural network approach to evaluate fold recognition results

·         LOOPP - Sequence to sequence, sequence to structure, and structure to structure alignment

·         SAM-T02 - HMM-based Protein Structure Prediction

·         Threader - Protein fold recognition

·         ProSup - Protein structure superimposition

·         SWEET - Constructing 3D models of saccharides from their sequences

Ab initio

·         HMMSTR/Rosetta - Prediction of protein structure from sequence

Assessing tertiary structure prediction

·         Anolea - Atomic Non-Local Environment Assessment

·         Biotech Validation Suite for Protein Structures

·         EVA - EValuation of Automatic protein structure prediction

·         LiveBench - Continuous Benchmarking of Structure Prediction Servers

·         PROCHECK - Verification of the stereochemical quality of a protein structure

·         What If - Protein structure analysis program for mutant prediction, structure verification, molecular graphics

Molecular modeling and visualization tools

·         Swiss-PdbViewer - A program to display, analyze and superimpose protein 3D structures

·         Astex Viewer

·         MolMol

·         Rasmol

·         VMD

Prediction of disordered regions

·         DisEMBL - Protein disorder prediction

·         GlobPlot - Protein disorder/order/globularity/domain predictor


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Revised: February 16, 2024