University of New Mexico Health Sciences Center
Genomics software available through the Division of Biocomputing.
Cheminformatics software available through the Division of Biocomputing.
| Visualizer | (1) | basic visual environment |
| Compare | (1) | compare and fit hypotheses onto molecules |
| ConFirm | (1) | conformational model generator |
| Databases | (1) | Maybridge, NCI |
| DBServer | (1) | queries above databases |
| HipHop | (1) | feature-based alignment tool for 3D QSAR and 3D search queries |
| HypoGen | (1) | generates 3D hypotheses to explain activity variations in structures of drug candidates |
| Info | (1) | build/administer databases of 3D structures |
| Shape | (1) | identify compounds with similar 3D shapes to a reference conformation |
| Depict Toolkit | (1) | programming library supporting depiction (2D) and conformation (3D) objects |
| Fingerprint Toolkit | (1) | programming library providing chemical structure characterization via the fingerprint object |
| MayBridge | (1) | a database of approximately 45,000 substances sold by MayBridge that were synthesized for purposes of pharmaceutical or agrochemical experimentation |
| PCFILTERS (clogp, cmr) | (1) | programs providing estimation of hydrophobicity and polarizability |
| SMARTS Toolkit | (1) | programming library supporting substructure specification and recognition |
| SMILES Toolkit | (1) | programming library providing fundamental chemical information support for user programs |
| Felix-2D | (1) | spectral processing and analysis of 1D and 2D NMR data |
| Felix-Analytical | (1) | analytical spectral analysis and assignment tools |
| Felix-Assign | (2) | semi-automated analysis and assignment of multidimensional NMR data of biomolecules |
| Felix-Model | (1) | links model structures with NMR spectral data |
| Felix-ND | (1) | spectral processing and analysis of multidimensional NMR data (1D to 4D) |
| Visualizer | (3) | basic visual enviroment |
| Affinity | (1) | docking of ligands |
| Binding Site Analysis | (1) | identify and characterize a protein's binding site |
| Biopolymer | (1) | build/modify nucleic acids, peptides, polysaccharides, proteins |
| CHARMm | (1) | comprehensive force field and program for energy calculations; extensive parameter library |
| CFF | (1) | class II forcefield derived within a consistent quantum mechanical framework |
| DeCipher | (1) | high-level analysis tool |
| Discover | (3) | molecular mechanics/dynamics |
| Ludi | (1) | de novo design software |
| MODELER | (1) | automatically generate a refined homology model of a protein given only the sequence alignment to a known 3D protein structure |
| NMR Refine DGII | (1) | distance geometry method to generate 3D structures using NMR derived data |
| NMR Refine Advanced | (1) | advanced methods - simulated annealing, relaxation matrix - to generate 3D structures using NMR derived data |
| Search/Compare | (1) | generates and compares the conformations of different molecules |
| Control System Toolbox | design and analyze feedback control systems |
| Extended Symbolic Math Toolbox | perform computations using symbolic mathematics and variable precision arithmetic |
| Image Processing Toolbox | perform image processing, analysis, and algorithm development |
| MATLAB Compiler | convert MATLAB applications into stand-alone C and C++ code |
| Optimization Toolbox | solve standard and large-scale optimization problems |
| Signal Processing Toolbox | perform signal processing, analysis, and algorithm development |
| Simulink | design and simulate continuous- and discrete-time systems |
| Spline Toolbox | create and manipulate spline approximation models of data |
| Statistics Toolbox | apply statistical algorithms and probability models |
| Symbolic Math Toolbox | perform computations using symbolic mathematics and variable precision arithmetic |
| ISIS/Base | database system for chemical structures |
| ISIS/Draw | 2D drawing of chemical structures |
| GRID | molecular interaction field generation and docking |
| PENGUINS | virtual high throughput screening---fast library enumeration, filtering and docking |
| VolSurf | molecular interaction field analysis in pharmacokinetics |
| Filter | graph-based compound elimination tool |
| FRED | Fast Rigid Exhaustive Docking |
| Omega | rapid conformer generation |
| ROCS | shape matching and database search |
| SHAPE | shape toolkit |
| VIDA | visualization tool |
| ZAP | Poisson-Boltzmann electrostatics scoring function |
| SYBYL/Base | includes comprehensive tools for molecular modeling: structure building, optimization, and comparison; visualization of structures and associated data; annotation, hardcopy and screen capture capabilities; and a wide range of force fields |
| Advanced Computation | provides a wide range of tools for conformational analysis that enumerate all possible torsional states of a molecule or identify just its low-energy conformations |
| Biopolymer with FlexiDock | delivers an extensive set of tools for building, visualizing, manipulating, and predicting the 3D structure of biological molecules, including proteins, peptides, nucleic acids, and polysaccharides |
| Composer | builds 3D models of proteins from sequence using knowledge-based homology modeling methods |
| CPU | |
| DISCOtech | performs pharmacophore elucidation from precomputed conformations of active compounds that bind to the same target |
| Dynamics | |
| MatchMaker | uses a threading method to predict the 3D structure of proteins from amino acid sequence |
| ProTable | uses SYBYL's Molecular Spreadsheet to deliver tools that analyze and assess the quality of protein structures. Graphical rendering and linked display of tabular and graphical information help communicate the results of analyse |
| QSAR with CoMFA | provides tools needed to build statistical and graphical models of biological activity (or other properties) from molecular structures, and to use those models in making predictions for the activity of untested compounds |
| UNITY | a search and analysis system for the exploration of chemical databases and features rapid, conformationally flexible 3D searching |
| MODDE | chemometrics design of experiments |
| SIMCA-P+ | chemometrics megavariate data analysis |
| Protein ID | protein database |
| TurboSEQUEST | protein identification |
Division of Biocomputing
MSC11 6145
Research Incubator Building, Suite 170
2703 Frontier, NE
1 University of New Mexico
Albuquerque, NM 87131
USA
Phone (505)272-8223
Fax (505)272-0238
Contact Us via email
