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Molecular Modelling

Molecular Modelling

Molecular modeling (computer aided molecular design) is a software based technique to design a molecule, to compute its properties, and to mimic its behaviour.

Online available information resources on molecular modelling.

Further information categories about related topics are listed in the navigation menu on the left side of these page.

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Lecture Notes, Tutorials

Molecular Modelling of DNA - [e]

Molecular Modeling
Lecture slides: introduction into molecular modelling - Format: PDF - [e]

Organic Chemistry
Lecture notes: molecular modelling for organic chemistry - [e]

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Data and Databases

CDD - Conserved Domain Database
... is a protein annotation resource, which consists of a collection of well-annotated multiple sequence alignment models for ancient domains and full-length proteins. NCBI, USA - [e]

MMDB - Molecular Modelling DataBase
... a database of macromolecular 3D structures, as well as tools for their visualization and comparative analysis. NCBI - [e]

... is a database of small molecules, which provides information on their biological activities. NCBI - [e]

... is a database of structure-structure alignments. Each protein chain and 3D domain from MMDB is compared with all the others using the VAST (Vector Alignment Search Tool) algorithm. NCBI - [e]

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Software and Programs

Accelrys Software Inc.
... develops and commercializes scientific business intelligence software for the integration, mining, analysis, modeling and simulation, management and interactive reporting of scientific data - [e]

The Amsterdam Density Functional (ADF) package is software for first-principles electronic structure calculations. ADF is used by academic and industrial researchers in such diverse fields as pharmacochemistry and materials science. SCM, Netherlands - [e]

Assisted Model Building with Energy Refinement - [e]

... is a fully-featured semiempirical quantum mechanical program. Semichem, USA - [e]

Molecular modelling software. Agile Molecule, Sweden - [e]

... is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. Scripps Research Institute, USA - [e]

... is a versatile tool for constructing, analyzing and minimizing molecular structures. Biographics Laboratory - [e]

... is a molecular modeling and visualization program for personal computers - [e]

... is a versatile and widely used molecular simulation program with broad application to many-particle systems. Chemistry at HARvard Macromolecular Mechanics, USA - [e]

Chembrain XTE
Worldwide unique chemical database for three-dimensional molecular structures with integrated artificial intelligence capable of learning applicable in the prediction of any molecular properties as well as for use as laboratory notebook. Softonic - [d, e]

... is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. UCSF, USA - [e]

... is an advanced, fully featured Quantitative Structure/Activity Relationship (QSAR) program that ties information from AMPAC™ and other Quantum Mechanics programs with experimental data. Semichem, USA - [e]

... is a realtime 3D visualization program for structural biology data - [e]

With gOpenMol small molecules, and to lesser extent protein structures, as well as the chemical properties, total electron densities and molecule orbitals of small molecules can be visualized and analyzed.. CSC, Finland - [e]

General Molecular Modeling Software
List of General Molecular Modeling (CADD, CAMM, QM, etc.) Software. NetSci, USA - [e]

GOLPE (Generating Optimal Linear PLS Estimations) is the state of the art chemometric toolbox for 3D QSAR. Multivariate Infometric Analysis S.r.l., Italy - [e]

... is a computational procedure for determining energetically favourable binding sites on molecules of known structure. Molecular Discovery Ltd., USA - [e]

... is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles - [e]

... has a multi-window, multi-functional, project, and GUI approach to protein sequences. It creates multi-sequence alignments, phylogenetic trees and models molecular evolution. It enables studies of the relationship between protein sequence and protein structure. HyperCube, Inc., USA - [e]

The ICM-Browser provides a biologist or a chemist with direct access to the treasures of structural biology and protein families. Molsoft, USA - [e]

MathMol - Mathematics and Molecules
... is designed to serve as an introductory starting point for those interested in the field of molecular modeling - [e]

Molecular Display and Simulation System. UCSF, USA - [e]

Molecular Modelling Toolkit, MMTK
... is an Open Source program library for molecular simulation applications. In addition to providing ready-to-use implementations of standard algorithms, MMTK serves as a code basis that can be easily extended and modified to deal with standard and non-standard problems in molecular simulations - [e]

Molecular Networks
... provides multifaceted, innovative software to the chemical, biotechnology and pharmaceutical industry. The company's suite of chemoinformatics applications covers many different areas including: handling of chemical information, design of new chemical entities and prediction of physicochemical and biological properties of chemical compounds - [e]

The program system MOLGEN is devoted to generating all structures (connectivity isomers, constitutions) that correspond to a given molecular formula, with optional further restrictions, e.g. presence or absence of particular substructures - [e]

... is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations. Avatar Software, Sweden - [e]

... is a full-featured molecular modeling and visualization tool designed for Windows. New River Kinematics, USA - [e]

Molecular Visualization Resources; all free and open source, collected by Eric Martz, including all Martz-authored molecular visualization projects - [e]

NAMD - Molecular Dynamics Simulator
... is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems - [e]

... is a USER-SPONSORED molecular visualization system on an OPEN-SOURCE foundation. DeLano Scientific LLC, USA - [e]

... is an innovative receptor-modeling technology which is based on a novel scoring function including hydrophobicity, hydrogen bonding, entropy and the quantification of explicitly simulated induced fit. Biographics Laboratory, Switzerland - [e]

Molecular Visualization Freeware - [e]

... is a set of tools for generating high quality raster images of proteins or other molecules - [e]

... provides accurate, reliable, and high performance computational technology to solve real-world problems in life science research - [e]

With unsurpassed visualization and a wide range of well documented computational methods in a single user-friendly software tool, Spartan delivers the full power of molecular modeling to chemists everywhere. Wavefunction, Inc., USA - [e]

... is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface - [e]

TINKER - Software Tools for Molecular Design
... is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers - [e]

... was originally developed to create a bridge between most of the molecular software packages only, but in the years, enhancing its features, it's evolved to a complete molecular modelling suite - [e]

VMD - Molecular Graphics Viewer
... is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting - [e]

... is a molecular-graphics, -modeling and -simulation program - [e]

... is a molecular mechanics program for modeling proteins and small-molecule protein complexes. Biographics Laboratory, Switzerland - [e]

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Journal of Computer-Aided Molecular Design
... provides a form for disseminating information on both the theory and the application of computer-based methods in the analysis and design of molecules. Springer - [e]

Journal of Molecular Graphics and Modelling
... is devoted to the publication of papers on the uses of computers in theoretical investigations of molecular structure, function, interaction, and design. Elsevier - [e]

Journal of Molecular Modeling
... covers all aspects of molecular modeling including life science modeling; materials modeling; new methods; and computational chemistry. Springer - [e]

Journal of Molecular Structure
... is dedicated to the publication of full-length articles and review papers, providing important new structural information on all types of chemical species. Elsevier - [e]

Journal of Molecular Structure: Theochem
... publishes research related to the broad area of theoretical and computational investigation of molecular systems, including problems of molecular structure, properties, energetics, reactions, interactions, and dynamics. Elsevier - [e]

Molecular Simulation
... covers all aspects of research related to, or of importance to, molecular modelling and simulation (including informatics, theoretical and experimental work). Taylor and Francis, UK - [e]

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Research facilities and departments

Switzerland: Basel
Molecular Modeling. University of Basel, Switzerland - [e]

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Cheminformatics and QSAR Society
... of scientists who are involved in Cheminformatics, and/or investigate quantitative structure-activity relationships in medicinal, agricultural, or environmental chemistry - [e]

ChemVis - Chemical Visualization on the Internet
ChemVis proposes the development of an Internet standard orientated system for the embedding of dynamic visualizations in digital documents in the field of chemistry - [d, e]

Darmstadt Molecular Modeling Workshop
Every year, the organisers welcome both poster or lecture contributions in English or German from all areas of molecular modeling including life sciences, physical sciences, material sciences and the nano sciences - [e]

Molecular Modelling Group: To stimulate the use and application of molecular modelling and related methods in Industry - [e]

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Molecular Modelling
Molecular, modelling, computer, aided, molecular, design, methods, techniques, basics, theory, software, research
01.03.2012 00:00:00 [link check]
01.03.2012 [site update]

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Related Books and Scientific Literature: Molecular Modelling:


Hans-Dieter Höltje, Wolfgang Sippl, Didier Rognan, Gerd Folkers

Molecular Modeling: Basic Principles and Applications

Ideal for beginners, this book explains the basics of modeling in a competent yet easily understandable way. Following complete sections on the modeling of small molecules, protein modeling and chemogenomics, completely worked-out examples show the way to the reader's first modeling experiment.

This new, third edition features a new chapter on chemogenomics, reflecting the trend towards 'chemical biology', as well as the protein modeling example being completely rewritten for a better 'feel' of modeling complex biomolecules.

The authors are experienced university teachers who regularly hold courses on molecular modeling, making this a tried-and-tested text for teachers. It is equally valuable for experts, since it is the only book to evaluate the strengths and limitations of the molecular modeling techniques and software currently available.

Wiley-VCH; 2008

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