Biology

Hackert Research Groups Hackert Research Groups- Includes brief lecture notes, exam papers, and related links. Molecular Biology Molecular Biology- Details of course run at Davidson, North Carolina. Claude Aflalo Claude Aflalo- Personal page of this Senior Lecturer at the Ben-Gurion University of the Negev, Beer Sheva, Israel. Includes resources on biochemistry and learning strategies. Als… Pande Group Pande Group- Folding simulations for fusion peptides, proteins and RNA with aim of predicting structure from genome by research at Stanford University, California. AutoDock AutoDock- A suite of automated docking tools. It is designed to predict how small flexible molecules, such as substrates or drug candidates, bind to a receptor of known 3D structu… EGO EGO- A parallel program for molecular dynamics simulations of biomolecules. B: On-line Molecular Modeling B: On-line Molecular Modeling- "B" (formerly known as Biomer) is a Java-based molecular modeling program for small organic molecules and biopolymers. Supports nucleic acids (DNA/R… Ascalaph Designer Ascalaph Designer- Program for creating molecular models, molecular mechanics simulations and development of the force fields by quantum chemical methods. Abalone Abalone- Program for bio-molecular modeling, particularly for molecular graphics and dynamics with implicit and explicit water models. The Jalview Internal PDB Viewer The Jalview Internal PDB Viewer- Used to visualize three dimensional structure of macromolecules, using protein data bank format for atom coordinates. GrAfSS: Graph Theoretic Applications for Structure Searching GrAfSS: Graph Theoretic Applications for Structure Searching- Graph theoretic methods for the analysis of structural relationships in biological macromolecules. Prion Helical Wheels Prion Helical Wheels- Java applet to illustrate alpha-helices, using a traditional helical wheel. Output as Postscript, JPEG, GIF or PICT. Gromacs Gromacs- A molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids. It is a free software. ZMM Software Inc. ZMM Software Inc.- Modeling tool for theoretical studies, employing molecular mechanics approach in combination with Monte Carlo energy minimization algorithm. Downloads on secure… WhatIf WhatIf- Protein structure analysis software for Linux, SGI/IRIX, Windows NT. Performs mutant prediction, structure verification, homology modeling and molecular visualization. Lin… Jay Ponder Lab Jay Ponder Lab- Graphical user interface to suites of molecular modeling tools, providing an integrated environment for engineering applications. Contacts for the group at Washing… Sesame Project Sesame Project- Protein structure-function software in multiple modules, maintained at the University of Wisconsin, Madison. ChemVis ChemVis- Visualization of physico-chemical structures in VML, from research at the Universities of Stuttgart and Erlangen in Nürnberg, Germany. YASARA YASARA- (Yet Another Scientific Artificial Reality Application) is an interactive real-time molecular dynamics program. NAMD NAMD- A parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes s… X-plor Archives X-plor Archives- Forum for 3D macromolecular structure determination. Includes links to other Biosci/Bionet newsgroups, maintained at Indiana University, Bloomington. TINKER TINKER- A free molecular modeling package for molecular mechanics and dynamics, with some special features for biopolymers. Distributed as source code and as binaries for Windows9… Folding@home Folding@home- It is a distributed computing project which studies protein folding, misfolding, aggregation, and related diseases. Zhen Huang's Laboratory Zhen Huang's Laboratory- X-ray crystallography of selenium derivatization in DNA and RNA, enzymology of T7 RNA polymerase and ribozymes. Lists members, related links and contacts … Schepartz Laboratory Schepartz Laboratory- Projects on intracellular interfacing of proteins and DNA, transcription factors, effects of viral attack and mimickery. Includes publications and member con… Wang, Shaomeng Wang, Shaomeng- Includes a list of publications, grants, group members, overview of labs, former members, software, and reagent inventory, at University of Michigan, Ann Arbor. The HeliX group The HeliX group- Introduction to the X-ray crystallographic work on nucleic acid and protein structure. Includes poster presentations, publications list and profiles of staff in t… MRC Laboratory of Molecular Biology MRC Laboratory of Molecular Biology- Introduction, history, openings, and projects in neurobiology, cell and structural biology, and protein and nucleic acid chemistry, in Cambrid… Carbohydrate-Active Enzymes Carbohydrate-Active Enzymes- The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding functional domains of enzymes that degrade, modify… BRENDA BRENDA- Comprehensive enzyme information system, searchable by a number of different parameters. PhytAMP database PhytAMP database- Data repository of plant natural antimicrobial peptides. Wikipedia: Protein Biosynthesis Wikipedia: Protein Biosynthesis- Article summarising the process by which the cell converts the DNA sequence to proteins. Wikipedia: Posttranslational Modification Wikipedia: Posttranslational Modification- Article on chemical modification of polypeptide chains after synthesis. ATP Synthase ATP Synthase- Includes the enzyme's history, general information, news, research, links, and FAQ. Graether, Steffen, PhD. Graether, Steffen, PhD.- CV, publication list and introduction to research studying the structure and function of antifreeze proteins. Professor in Molecular and Cellular Biology … The Cyclotide Webpage The Cyclotide Webpage- Classification, properties, potential applications and research on polypeptides characterized by their cyclised backbone, with an embedded cystine knot, mai… ATPases Associated with Cellular Activities (AAA) ATPases Associated with Cellular Activities (AAA)- Information and databases on the ubiquitous AAA protein superfamily, essential for cell cycle, vesicular transport, mitochondria… Attractin Attractin- Resource, including its relationship to immunity, pigmentation, neurochemistry, obesity, mutations resulting in the genotypes of mahogany, zitter, myelin vacuolation an… Fiberlab Fiberlab- Laboratory to investigate fiber-forming spiders, mussel collagen, nanoproteinfibers, and prions at Munich, Germany. ISTH SSC VWF Information Homepage ISTH SSC VWF Information Homepage- Genetic mutation and polymorphism database for human von Willebrand factor with other useful information for researchers, from the University of… Nucleic Acids Symposium Series Nucleic Acids Symposium Series- Supplementary publication to Nucleic Acids Research. Nucleic Acid Database Nucleic Acid Database- Assembles and distributes structural information about nucleic acids. Includes databases, tutorials, and a musical atlas using different musical algorithms … Mobile Group II Introns Mobile Group II Introns- Phylogenetic tree, secondary and ORF structure to identify and catalog group II introns in bacteria and other organisms, maintained by the Zimmerly Labora… DOE Joint Genome Institute DOE Joint Genome Institute- Dynamic comparative analysis of the human and mouse genomes. Includes introduction to genomics, historical timeline and poster, operated for the Depart… Structure Structure- Monthly publication of papers, back to 1994, on structural investigations in cell and molecular biology. PDF and full text subscription options from Cell Press. Bioorganic Chemistry Bioorganic Chemistry- Publishing original research at the interface of chemistry and biology, this journal presents articles where the principles and techniques of organic and phy… Ancient Biomolecules Ancient Biomolecules- Publishes articles about the discovery of previously undetected molecules in ancient biological material, stability studies, characterization of decay produc… Overview of Lipid Metabolism Overview of Lipid Metabolism- Provides information on lipids, the major apoproteins and enzymes important to their metabolism, and their physiology from Merck Manual. Carbohydrates: Chemical Structure Carbohydrates: Chemical Structure- Educational site describing the structures of sugars, starches, cellulose and other compounds of carbon, hydrogen and oxygen found in living org… Functional Glycomics Gateway Functional Glycomics Gateway- Collaboration between the Consortium for Functional Glycomics and Nature Publishing Group. Includes glycomics news, resources, and databases of glyca…