Guide of LIGAND DESIGN
Welcome to Axiom Discovery
Develops software and offers consulting services for in-silico drug discovery
and molecular visualization.
See how Axiom Discovery software aids drug discovery - from modeling to de-novo ligand design Record, organize, and share research throughout your organization Download free software | © 2004 Axiom Discovery, Inc
Linux4Chemistry - Linux software for chemistry: molecular modeling ...
An up-to-date website with the links to Linux software for chemistry including
computational, visualization, graphic, molecular modeling, both free and ...
These are a new generation of 3D-molecular descriptors with application in 3D-QSAR, QSAR, virtual screening, design of combinatorial libraries, selectivity studies and in any field where 3D quantitative pharmacophoric description for (macro)molecules is needed
Cheminformatics ALOGPS provides prediction of logP and aqueous solubility of compounds to be used in drug design (ADMET and HTS) and environmental chemistry studies
Molecular Dynamics AmberFFC is designed to convert the different existing AMBER force fields (FF) freely available in the public domain, for use with commercial molecular modeling packages, using the MSI software package as a case model
It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure
Cheminformatics Babel is a program designed to interconvert a number of file formats used in molecular modeling
Crystallography, NMR CNS (Crystallography & NMR System) is a software suite designed to provide a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination
The programs are designed primarily for extended multi-reference (MR) calculations on electronic ground and excited states of atoms and molecules
International Journal of Chemical Kinetics
Publishes original research in gas phase, condensed phase, and polymer reaction
kinetics, as well as biochemical and surface kinetics.
International Journal of Quantum Chemistry
Publishes original papers with emphasis on formal and computational quantum
mechanics and its application to the theory and modeling of the structure and ...
info: LIGAND DESIGN
Photo by www.chem.leeds.ac.uk
Ligand-Gated Ion Channel Database
LGICdb is a curated repository of genes coding for subunits of Ligand-Gated Ion
Channels.
You can also design your own entry with the
MDB (Main Page) - Metalloprotein Site Database & Browser, TSRI
Resources for coordination patterns, and estimating distance between metal and
ligand at binding sites. Includes search and visualization interfaces, ...
This database is being developed as part of a project whose ultimate goal is metalloprotein design, allowing the interactive visualization of geometrical and functional information garnered from the MDB
Use the interactive interface to search the MDB Site: | Metalloprotein Structure and Design Site: | Page maintained by Jesus M
William L. Jorgensen Research Group - Welcome to the Jorgensen Lab
Studies of organic reactions in solution and in enzymes using Monte Carlo and
semiempirical QM/MM simulations. (Yale University)
1987- MD and MC for proteins, denaturation, enzymatic rxns 1996- FEP/MC for protein-ligand binding 1997- Full QM/MM for organic & enzymatic reactions 2000- Structure-based drug design, ADME predictions 2001- Semiempirical molecular orbital method development 2003- Polypeptide and nucleic acid folding Newest publications 302
Computer-aided design of non-nucleoside inhibitors of HIV-1 reverse transcriptase
Jorgensen Research Group Dept of Chemistry, Yale University New Haven, CT 06520-8107, USA Phone: (203)432-6288 Fax: (203)432-6144 Webmaster: Laura Thomas Design:
Curt M. Breneman
Automated design and discovery of novel pharmaceuticals using semi-supervised
learning in large molecular databases. Ab initio methods, data mining, and QSAR.
Kristin Bennett from the Math department, a cross-disciplinary effort is has been initiated to develop a new method for automated molecular design
The resulting models may then be used in inverse-QSAR design experiments to propose new molecular structures for evaluation
Automated Drug Discovery Methods and "Materials by Design" The development of the TAE-based molecular property descriptors led to some fruitful collaborations with members of the Statistics and Chemometrics communities
These interactions have resulted in a new set of automated molecular design tools which are currently undergoing parameterization and testing
Embrechts &“New Developments in PEST shape/property Hybrid Descriptors&”, Journal of Computer-Aided Molecular Design , 17 , 231-240, 2003
Cramer, "High Throughput Screening and Quantitative Structure-Efficacy Relationship Models for Designing Displacers for Anti-sense Oligonucleotide Purification in Anion-Exchange Systems", Separation Science and Technology
Embrechts, Muhsin Ozdemir, Larry Lockwood, Kristin Bennett, and Dirk DeVogelaere, "Feature Selection Methods Based on Genetic Algorithms for In Silico Drug Design, " Chapter 15 (26 pages) in Evolutionary Computation in Bioinformatics , Corne, D
Benefits
Photo by www.axiomdiscovery.com
GAUL: Genetic Algorithm Utility Library A programming library designed to aid development of applications that use genetic
algorithms.
It is designed to assist in the development of code that requires evolutionary algorithms
Introduction The Genetic Algorithm Utility Library (or, GAUL for short) is a flexible programming library designed to aid in the development of applications that use genetic, or evolutionary, algorithms
- De novo molecular design
- water site prediction, drug-design, protein folding
Faculty Members and Research Interests (SIIT.TU.)
List of SIIT faculty members and their research interests. With links to personal
info page and email.
of Akron) Photo-catalytic synthesis of hydrocarbons from CO2/H2O, Gas-solid reactor design, Heterogeneous Catalysis, Nano-material / zeolite syntheses, Bio-molecular imprinted material
of Tokyo) Application of Three-Dimensional Finite Element Method to Design of Steel Structures; Development of Run-of-River Small Hydropower Projects
(UMIST) Analogue circuit design, Very Large Scale Integration (VLSI)
(Penn State Univ.) Multidimensional systems and signal processing, Robust control, Image processing, Minimax controller design, Wavelet and filter bank
(Osaka Univ.) Power systems control & stabilization, FACTS applications, Robust control application to design of power system controllers
(Princeton Univ.) Communication systems, Spread-spectrum systems, Wireless communications, Signal processing, Digital filter design and realization
(Osaka Univ.) Broadband communication networks, Network reliability analysis, Self-healing network design, ATM and TCP/IP technologies, Congestion control technologies
of Texas, Arlington) Industrial ergonomics, Product and workstation design, Industrial noise
Inst.) Steam boilers (computation and design); Combustion and emission control in boilers fired with fossil fuels; Combustion of biomass fuels in FBC
Flexible molecular docking software. Drug Discovery virtual ...
Provides drug discovery using computational technology to simulates intermolecular
interactions.
American Chemical Society Publications: Journal of the American ...
Publishes recent advances in all areas of chemical research.
Sakmar, Amiram Hirshfeld, and Mordechai Sheves pp 10503 - 10512; (Article) DOI: Full: / (599K) Rational Design of Bacitracin A Derivatives by Incorporating Natural Product Derived Heterocycles Björn Wagner, Dirk Schumann, Uwe Linne, Ulrich Koert, and Mohamed A
LIGAND DESIGN ?
American Chemical Society Publications: Journal of Medicinal ...
Ppublishes original research on the correlation of molecular structure with
biological activity.
Saeh pp 4805 - 4808; (Letter) DOI: Full: / (47K) Highly Potent and Selective Histone Deacetylase 6 Inhibitors Designed Based on a Small-Molecular Substrate Takayoshi Suzuki, Akiyasu Kouketsu, Yukihiro Itoh, Shinya Hisakawa, Satoko Maeda, Minoru Yoshida, Hidehiko Nakagawa, and Naoki Miyata pp 4809 - 4812; (Letter) DOI: Full: / (135K) ARTICLES Potential Lead for an Alzheimer Drug: A Peptide That Blocks Intermolecular Interaction and Amyloid Protein-Induced Cytotoxicity Ju-Won Kwak, Hyun-Kyung Kim, and Chi-Bom Chae pp 4813 - 4817; (Article) DOI: Full: / (189K) Synthesis of Trifluoromethylaryl Diazirine and Benzophenone Derivatives of Etomidate that Are Potent General Anesthetics and Effective Photolabels for Probing Sites on Ligand-Gated Ion Channels S
Denny pp 4896 - 4911; (Article) DOI: Full: / (390K) Structural Insights into Monoamine Oxidase Inhibitory Potency and Selectivity of 7-Substituted Coumarins from Ligand- and Target-Based Approaches Marco Catto, Orazio Nicolotti, Francesco Leonetti, Andrea Carotti, Angelo Danilo Favia, Ramón Soto-Otero, Estefanía Méndez-Álvarez, and Angelo Carotti pp 4912 - 4925; (Article) DOI: Full: / (716K) In Vitro and in Vivo Magnetic Resonance Detection of Tumor Cells by Targeting Glutamine Transporters with Gd-Based Probes Simonetta Geninatti Crich, Claudia Cabella, Alessandro Barge, Simona Belfiore, Cristina Ghirelli, Luciano Lattuada, Stefania Lanzardo, Armando Mortillaro, Lorenzo Tei, Massimo Visigalli, Guido Forni, and Silvio Aime pp 4926 - 4936; (Article) DOI: Full: / (472K) Design of Inhibitors of Orotidine Monophosphate Decarboxylase Using Bioisosteric Replacement and Determination of Inhibition Kinetics Ewa Poduch, Angelica M
Institute of Molecular Function, Molfunction
Producer of Homology Modeling for HyperChem, Gaussian Interface for HyperChem,
ONIOM Interface for Receptor, and Docking Study with HyperChem.
All operations are fully automated in the GUI-based manner, and thus the program supports the logical molecular modeling, functional analysis, and simulations in the life science research such as the structure-based drug design, as well as an unexplored research
SensoPath Technologies, Inc - Home
Offers custom synthesized, novel tethers to attach proteins, DNA or small molecules
to biosensor surfaces. Includes catalog with formulas, terms and contacts in ...
Our core technology involves the design of robust multi-branched dendrimer molecules that can be attached as self-assembled monolayers (SAMs) to a variety of surfaces
The tethers and fluorophores can be custom designed for specific binding studies involving a ligand and any protein or small molecule having a functional group for attachment to the tether or dye terminus
Custom design is available, either to your specifications or in consultation with our synthetic chemists and biochemists Applications in which SensoPath products can enhance sensitivity and reliability: Surface Plasmon Resonance slides Quartz Crystal Microbalance sensors Gold nanoparticles Fiber optic and wave guide glass surfaces Atomic Force Microscopy single molecule probes Genomic and Proteomic microarray probes Electrophoresis and blot probes Tethers Antibodies that will recognize specific pathogenic agents can be immobilized on self-assembled monolayers (SAMs) consisting of a tether molecule specifically designed for a sensor surface
(DePew, NY) surface plasmon resonance (SPR) system for which they can be custom designed and applied
IN THE BELOW CATALOG, WE OFFER MATERIALS FOR THE DESIGN AND FABRICATION OF SAMs FOR BIOMEDICAL RESEARCH STUDIES AND TETHERS FOR ATOMIC FORCE MICROSCOPY APPPLICATIONS WE INTRODUCE THE FIRST OF A FAMILY OF HIGH QUANTUM YIELD 1-AND 2-PHOTON WATER-SOLUBLE FLUOROPHORES FUNCTIONALIZED FOR COUPLING TO PROTEINS OR NUCLEIC ACIDS
Structure, function and mechanism of cytochrome P450; drug ...
Structure, function, mechanism and regulation of the drug and carcinogen metabolizing
cytochrome P450 enzymes are studied by biochemical, biophysical and ...
Implications for the design of selective chemotherapeutic agents
Pincus, M.R., Brandt-Rauf, P.W., Michl, J., Carty, RP and Friedman, F.K.: ras-p21-induced cell transformation: unique signal transduction pathways and implications for the design of new chemotherapeutic agents
eLABorate Packages
Programs designed as educational exercise for planning experiments in enzyme
kinetics, protein-ligand binding, protein purification and related projects from ...
Packages from York an exercise in the design and planning of experiments in enzyme kinetics empirical investigation of basic statistical procedures a simulation of a high field FT-NMR spectrometer an investigation of the basic principles of equilibrium electrochemistry investigation of bacterial protein and nucleic acid synthesis Packages from Leeds purification of proteins visual simulation of protein-ligand binding Packages from Surrey an information resource for practical chemistry simulations of chemical reaction kinetics Packages from Oxford using antibodies for quantitative assays (really two packages in one: riaLAB and elisaLAB ) Go back to the
Pande Group
Folding simulations for fusion peptides, proteins and RNA with aim of predicting
structure from genome by research at Stanford University, California.
Faculty of Biological Sciences | Home
One of the three academic schools of the Faculty of Biological Sciences.
Browse Available ETDs by Author: all
Searchable and browsable repository of theses and dissertations from Caltech.
Home @CallCenter