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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

ALP Windows
Automated Linkage Preprocessor. Determines sizes of microsatellite fragments separated on an A.L.F. Sequencer (Pharmacia Biotech), removes stutter, performs genotyping and Mendelian checks, and formats data for Lathrop's Linkage Program Package.
Web Site Home Web Site: MRC Human Genetics Unit

AMBER Unix
AMBER 6 is a molecular simulation program.The academic price for licensing is the same as for AMBER 5, $400. (This fee may be reduced or waived in special circumstances.) The industrial price is $20,000 for new licensees and $15,000 for those who have licensed AMBER 5.
Web Site Home Web Site: AMBER web-page

AMMP Linux  Unix  Windows
AMMP is a modern full-featured molecular mechanics , dynamics and modeling program. It can manipulate both small molecules and macromolecules including proteins, nucleic acids and other polymers. It is written in C and has been ported to many different computers. The source code is available under the GNU copyleft.
Web Site Home Web Site: Kimmel Cancer Center

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

AlleleID 4 Mac  Windows
AlleleID supports real time PCR primer design, design of TaqMan, SYBR Green primer design, TaqMan MGB probe design and design of microarrays for detecting gene splicing and alternative splicing. AlleleID can be used to design cross species assays, assays for bacterial identification, species identification and strain detection. You can align the nucleotide sequences to locate differences in DNA and to find unique or conserved regions and then design oligos to amplify and detect either species or strains of interest from the mix. AlleleID also supports assays for selectively amplifying cDNA from gDNA.
Web Site Home Web Site: PREMIER Biosoft

AlleleID 5
AlleleID designs real time PCR and microarray probes and primers for identifying strains and sequences from an alignment and for amplifying and detecting patterns across sequences. AlleleID has a built-in ClustalW alignment module which aligns the nucleotide sequences. You can choose to amplify and detect sequence specific or conserved regions from the mix. AlleleID supports TaqMan, molecular beacons, Fret, TaqMan MGB and Microarray probes. A distinguishing feature of AlleleID is the ability to design real time PCR primers and probes to spot and amplify exons/introns
Web Site Home Web Site: Premier Biosoft

AmiraMol Linux  Unix  Windows
Together with Amira 2.3, an object-oriented interactive system for 3D data visualization, the new extension AmiraMol has been released. AmiraMol adds advanced tools for the visualization of Molecules. It combines Amira's strong capabilities for 3D data visualization like hardware accelerated volume rendering with specific tools for molecular visualization and data analysis. AmiraMol is available for Windows, Linux, IRIX, HP-UX, and SunOS. To get more information or to download a free trial version of Amira please visit our website:
Web Site Home Web Site: AmiraMol

Ascalaph Linux  Windows
Molecular Modelling Suite. * Molecular Design * Molecular mechanics simulations * Quantum calculations * Force Field development * GPU accelerated Molecular Dynamics
Web Site Home Web Site: Agile Molecule

Ascalaph Quantum Windows
3D graphic interface for the Quantum Mechanics program PC GAMESS. Ascalaph Quantum provides the generation and editing of molecular models.
Web Site Home Web Site: Agile Molecule

AutoDock Linux  Mac  Unix
AutoDock is a suite of programs designed to predict the bound conformation(s) of a flexible ligand to a macromolecular target of known structure, like an enzyme or DNA. Is free to academics and educational institutions.
Web Site Home Web Site: AutoDock Home Page

Babel 1.6 MS-DOS  Unix  Windows
Babel is a program designed to interconvert a number of file formats currently used in molecular modeling. Babel is capable of assigning hybridization, bond order, and connectivity when these elements are not present in the input file. Babel has the ability to add and delete hydrogens from any file format.
Web Site Home Web Site: OpenEye Scientific Software

Beacon Designer Free Edition Internet Browser
Beacon Designer Free Edition is a free web based oligo properties calculator for analysing SYBR Green Primers and TaqMan Probes for possible secoondary structures such and for accurately calculating Primer and Probe Tm. Beacon Designer free edition also displays sequence details such as sequence length, runs, repeats, reverse, reverse complement and GC%.
Web Site Home Web Site: Premier Biosoft

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

Biomer Linux  Mac  Unix  Windows
Biomer is a web-based molecular modeling program written in Java. Version 1.0a includes biopolymer builders, force field driven geometry optimizations, and simulated annealing with molecular dynamics.
Web Site Home Web Site: Scripps Research Institute

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

CCP4 Unix  VMS
The CCP4 Program Suite is an integrated set of programs for protein crystallography, which performs Patterson search and refinement, isomorphous and molecular replacement, and structure refinement. It is distributed in source form (mostly Fortran), supported for VMS and various Unix platforms.
Web Site Home Web Site: Daresbury Laboratory

CHARMM Unix
An integrated macromolecular science package incorporating molecular simulation methodologies. We distribute the source code of the CHARMM program with documentation to individual academic research groups for a $600 licensing fee.
Web Site Home Web Site: The CHARMM Development Project

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 Gene Workbench Linux  Mac  Windows
CLC Gene Workbench 1.0 provides a wide range of advanced DNA sequence analyses, and is based on the same user-friendly and integrated software environment as CLC Free Workbench. Some analyses are - Assembly of DNA sequencing data - Advanced primer design - Molecular cloning - Automatic SNP annotation of sequences - 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 - Searches on GenBank 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

CNSsolve Linux  Unix
Crystallography & NMR System (CNS) is the result of an international collaborative effort among several research groups. The program has been designed to provide a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination. Highlights include heavy atom searching, experimental phasing (including MAD and MIR), density modification, crystallographic refinement with maximum likelihood targets, and NMR structure calculation using NOEs, J-coupling, chemical shift, and dipolar coupling data. Free for Academic (Non-Profit) Institutions (source code included).
Web Site Home Web Site: Brunger lab

CONCOORD Unix
CONCOORD is a method to generate protein conformations around a known structure based on distance restrictions. CONCOORD is available in gzipped tar format.
Web Site Home Web Site: The MD Group

Cell Electrophysiology Simulation Environment (CESE) Linux  Mac  Unix  Windows
Cell Electrophysiology Simulation Environment (CESE) is a comprehensive framework specifically designed to perform computational electrophysiological simulations, for example, simulations of cardiac myocyte electrical activity. CESE is useful for simulations of action potentials, individual ionic currents, and changes in ionic concentrations.
Web Site Home Web Site: Cell Electrophysiology Simulation Environment

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