Created by: Hande Küçük McGinty, Janice Kranz, Joseph Ostrow, Alex Clark, Yu Lin, Saminda Abeyruwan, Uma Vempati, Kunie Sakurai, Vance Lemmon, Ubbo Visser, John Turner, Stephan Schurer*
Contact: Stephan Schurer stephan dot schurer at gmail dot com
Method based on the application of information technology to chemistry and biology.
Method based on application of information technology to the field of molecular biology.
computational analysis of gene expression
Computational methods used for analysis of microarrays, expressed cDNA sequence tag (EST) sequencing, serial analysis of gene expression (SAGE) tag sequencing, massively parallel signature sequencing (MPSS), or various applications of multiplexed in-situ hybridization.
computational analysis of protein expression
Computational methods involved in analysis of protein microarrays and high throughput (HT) mass spectrometry (MS).
Computational methods involved in construction and interpretation of phylogenetic trees, which are used to classify the evolutionary relationships between homologous genes represented in the genomes of divergent species.
Software for evolutionary biology, designed to help biologists analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis.
Program for inferring phylogenetic trees or, more generally, phylogenetic networks from various types of data such as a sequence alignment, a distance matrix or a set of trees.
is a free computer program for the likelihood-based reconstruction of phylogenetic trees from molecular sequences.
A free Computational phylogenetics package of programs for inferring evolutionary trees (phylogenies).
Computational methods used to arrange the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences.
Global alignments, which attempt to align every residue in every sequence, are most useful when the sequences in the query set are similar and of roughly equal size.
Pairwise global alignment with whole genomes.
Local alignments are more useful for dissimilar sequences that are suspected to contain regions of similarity or similar sequence motifs within their larger sequence context.
Local search with fast k-tuple heuristic, slower but more sensitive than BLAST.
Local search with fast k-tuple heuristic.
Multiple sequence alignment computer program.
is a multiple sequence alignment program suitable for the alignment of large numbers of DNA sequences.
Multiple sequence alignment is an extension of pairwise alignment to incorporate more than two sequences at a time.
Pairwise sequence alignment methods are used to find the best-matching piecewise (local) or global alignments of two query sequences.
is an open source Java implementation of the Smith-Waterman algorithm with Gotoh's improvement for biological local pairwise sequence alignment using the affine gap penalty model.
Methods using of computer and informational techniques for problems in the field of chemistry
Consists of the exploration of energetically favorable spatial arrangements (shapes) of a molecule (conformations).
Set of criteria for predicting the oral bioavailability of a compound on the basis of simple molecular features (molecular weight, CLogP, numbers of hydrogen- bond donors and acceptors).
Library design enables access to the large number of drug- like molecules that could theoretically be made and can serve several purposes: for example, to generate a maximally diverse virtual library for lead generation, a biased library aimed at a specific target or target family, or a lead optimization library.
The design of bioactive compounds by incremental construction of a ligand model within a model of the receptor or enzyme active site, the structure of which is known from X-ray or NMR data.
computer simulation method by force field
A set of functions and parametrization used in molecular mechanics calculations.
second generation force field simulation
a simulations procedure, in which the system is allowed to equilibrate at high temperatures, and then cooled down slowly to remove kinetic energy and to permit trajectories to settle into local minimum energy conformations.
A simulation procedure consisting of the computation of the motion of atoms in a molecule or of individual atoms or molecules in solids, liquids and gases, according to Newton's laws of motion. The forces acting on the atoms, required to simulate their motions, are generally calculated using molecular mechanics force fields.
constraint molecular dynamics simulation
ab initio quantum chemistry computational method
Methods of quantum mechanical calculations independent of any experiment other than the determination of fundamental constants. The methods are based on the use of the full Schr
quadratic configuration interaction method
semi-empirical quantum chemistry computational method
Use parameters derived from experimental data to simplify computations.
Zerner's intermediate neglect of differential overlap
intermediate neglect of differential overlap
modified neglect of differential overlap
Selection of compounds by evaluating their desirability in a computational model.
The ligand-based ensemble of steric and electronic features that is necessary to ensure the optimal supramolecular interactions with a specific biological target structure and to trigger (or to block) its biological response.
Method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex.
potentials of mean force scoring function
The receptor-based ensemble of steric and electronic features that is necessary to ensure the optimal supramolecular interactions with a specific biological target structure and to trigger (or to block) its biological response.