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3-Dee Internet Browser
3 Dee is a database of protein domain definitions.
Web Site Home Web Site: EBI

3D Crunch Internet Browser
3DCrunch is a Very Large Scale Protein Modelling Project, which was run from May 18 to 20 at the Silicon Graphics Advanced Technology Center in Cortaillod (Ne) Switzerland.The aim of 3Dcrunch is to submit all entries of the SWISS-PROT and trEMBL databases to SWISS-MODEL. Furthermore, all sequences of bacterial origin will be submitted to fold the recognition algorithm implemented in FoldFit. Taken together, these approaches will yield structural models for all sequences with clear similarities to proteins of know 3-D structure and a suggested fold class for all bacterial sequences.
Web Site Home Web Site: Expasy

3D-PSSM Internet Browser  Windows
Protein fold recognition using 1D and 3D sequence profiles coupled with secondary structure information (Foldfit).
Web Site Home Web Site: Biomolecular Modelling Laboratory

AGM Build Linux  Windows
A molecular builder and conformational editor. AGM Build can be used for interactive model preparation for molecular dynamics simulations, including association of atom types and partial charges. Features: * Geometry editing * Lattice building * Building of chain molecules * Chains with predetermined conformations * Charges and atom types according to selected Force Field
Web Site Home Web Site: Agile Molecule

ANALYZE ii Linux  Unix
The ANALYZE package to classify conformations obtained from a global search into families and compute conformational characteristics such as RMS deviations and interproton distances. It can also estimate the statistical weights of the conformations by fitting the theoretically calculated average NOE intensities and coupling constants to the respective experimental data.
Web Site Home Web Site: Cornell University

ARP/wARP Unix
A program for the refinement of protein structures that combines in an iterative manner the reciprocal space structure factor refinement with updating of the model in real space.
Web Site Home Web Site: European Molecular Biology Laboratory

Abalone Windows
a program for biomolecular modeling. General Features: Molecular Dynamics, optimization, implicit and explicit water.
Web Site Home Web Site: Agile Molecule

Analytic Surface Calculation Internet Browser
EMBL's Analytic Surface Calculation Service calculates the surface of a given PDB structure.
Web Site Home Web Site: Bork Group, EMBL

Antibodies: Structure and Sequence Internet Browser
This page attempts to summarise useful information on antibody structure and sequence. It provides a query interface to the Kabat antibody sequence data, general information on antibodies and crystal structures and links to other antibody-related information.
Web Site Home Web Site: University College London

Atlas of Protein Side-chain Interactions Internet Browser
This atlas depicts how amino acid side-chains pack against one another within the known protein structures. This packing, which is governed by the interactions between the 20 different types of side-chains, determines the structure, function, and stability of proteins.
Web Site Home Web Site: Biomolecular Structure and Modelling Unit, University College London

BLAST 2.0 Internet Browser  MS-DOS
A tool used to identify any potential homologies of a given DNA or protein sequence with those stored in GenBank.
Web Site Home Web Site: NCBI

BioMedCAChe Linux  Mac  Unix  Windows
BioMedCAChe is a new computer-aided chemistry software package designed specifically for bio- and medicinal chemists. It provides powerful software tools to accelerate the drug discovery process. BioMedCAChe enables to analyze protein sequences and optimize their 3D structures, build protein structures by homology, dock ligands, and model enzyme reactions using whole enzymes.
Web Site Home Web Site: BioMedCAChe - Software for bio and medicinal Chemists

CAChe Linux  Mac  Unix  Windows
CAChe is a leading computer-aided chemistry modelling package designed for experimental chemists conducting research in life science, materials and chemical, as well as for undergraduate and graduate educators. CAChe lets every chemist visualize molecules in 3D, search for conformations, analyze chemical reactivity and predict properties of compounds with an easy-to-use, award-winning interface on desktop computers.
Web Site Home Web Site: Use CAChe to model your experiments

CLC Combined Workbench Linux  Mac  Windows
CLC Combined Workbench 1.0 aggregates all DNA sequence analyses of CLC Gene Workbench and all protein sequence analyses of CLC Protein Workbench. All analyses are fully integrated in one single, user-friendly, and intuitive software application. Some analyses are - Assembly of DNA sequencing data - Advanced primer design - Molecular cloning - Automatic SNP annotation of sequences - Secondary protein structure prediction - Signal Peptide Prediction (SignalP) - Transmembrane helix prediction (TMHMM) - Protein family analysis (PFAM) - 2 types of alignments - Phylogenetics - Motif search (known patterns) - Pattern discovery (unknown patterns) - BLAST - Batch processing of multiple analyses in one work-step - Dot plots - Hydrophobicity analyses - Antigenicity analyses - Searches on GenBank, SwissProt, TrEMBL, and PubMed - Detailed log of actions/analyses performed
Web Site Home Web Site: CLC bio

CLC Protein Workbench Linux  Mac  Windows
CLC Protein Workbench 1.5 provides a wide range of advanced protein sequence analyses, and is based on the same user-friendly and integrated software environment as CLC Free Workbench. Some analyses are - Advanced and integrated 3D molecular viewer - 2 types of alignments - Phylogenetics - Secondary protein structure prediction - Signal Peptide Prediction (SignalP) - Transmembrane helix prediction (TMHMM) - Motif search (known patterns) - Pattern discovery (unknown patterns) - BLAST - Batch processing of multiple analyses in one work-step - Protein family analysis (PFAM) - Dot plots - Hydrophobicity analyses - Antigenicity analyses - Searches on GenBank, Swiss-Prot, TrEMBL, and PubMed - Detailed log of actions/analyses performed
Web Site Home Web Site: CLC bio

Cath: Protein Structure Classification Internet Browser
CATH is a novel hierarchical classification of protein domain structures, which clusters proteins at four major levels, class(C), architecture(A), topology(T) and homologous superfamily (H). Class, derived from secondary structure content, is assigned for more than 90% of protein structures automatically. Architecture, which describes the gross orientation of secondary structures, independent of connectivities, is currently assigned manually. The topology level clusters structures according to their toplogical connections and numbers of secondary structures. The homologous superfamilies cluster proteins with highly similar structures and functions. The assignments of structures to toplogy families and homologous superfamilies are made by sequence and structure comparisons.
Web Site Home Web Site: Biomolecular Structure and Modelling Unit, University College London

Clusprot Internet Browser
CLUSPROT is a program that delineates spatial clusters in protein structures on the basis of atomic contacts between residues. The program allows for clustering of side-chains, main-chains, main-chains and side-chains, etc. The program reads files with protein structures that are in Brookhaven Protein Data Bank format.
Web Site Home Web Site: EMBL

DALI Internet Browser
The Dali server is a network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank.
Web Site Home Web Site: EBI

DAS Internet Browser
Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method.
Web Site Home Web Site: Stockholm University

DIG - Analysis, Reporting, Intelligence Linux  Unix  Windows
DIG is a Data Analysis, Reporting, Intelligence tool for data workers, labs, and webmasters. Use DIG to clean up duplicates, consolidate, trim, query, summarize large data set in Excel/Access, log files, Oracle, MySQL, lab or POS systems, or any databases. Comes with powerful Excel/Access add-ons, ad-hoc query & multi-dimensional analysis. Watch on-line demo, get a free 30-day trial, then pay $96/yr or $8/month.
Web Site Home Web Site: DigDB

DIRAC Unix
DIRAC is a FORTRAN (and a bit of C) code for relativistic molecular calculations based on the Dirac-Coulomb Hamiltonian. It solves the the 4-component Dirac-Hartree-Fock (DHF) equations by the Self Consistent Field (SCF) iterative procedure and provides tools for analysis of the converged wave function.
Web Site Home Web Site: Dirac's Homepage

DOWSER Unix
The Dowser program surveys a protein molecule's structure to locate internal cavities and assess the hydrophilicity of these cavities in terms of the energy of interaction of a water molecule with the surrounding atoms.
Web Site Home Web Site: University of North Carolina

Dang Unix
Reads coordinates from a Protein DataBank (PDB) molecular structure file and generates a table of several useful geometric measurements for each residue or base.
Web Site Home Web Site: J.M. Word, Duke University

Database of Macromolecular Movements Internet Browser
Searchable database of the motions that occur in proteins and other macromolecules, particularly using movies. Associated with it are a variety of free software tools and servers for structural analysis.
Web Site Home Web Site: Yale University

DomainFinder 1.0 Linux  Unix
A program for the determination and characterization of dynamical domains in proteins. For common operations it makes use of the Molecular Modeling Toolkit, a library of Python code for molecular modelling and simulation applications. Is an Open Source program.
Web Site Home Web Site: Theoretical biophysics at the CBM

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