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Links tagged with 'x-ray crystallography'

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Found 21 links

Displaying 15 links

AD-ENMTool Content

http://enm.lobos.nih.gov

Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Molecular Dynamics and Docking

Analysis of Dynamics of Elastic Network Model (AD-ENM) predicts the conformational changes a given protein structure can undergo.

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tagsactins adenosine triphosphate animals binding sites biophysical phenomena biophysics dictyostelium dna polymerase beta dna-directed rna polymerases elasticity humans kinesin ligands mice molecular conformation molecular models molecular motor proteins myosins nucleotides principal component analysis protein binding protein conformation proton-translocating atpases protozoan proteins secondary protein structure statistical models structure-activity relationship taq polymerase tertiary protein structure theoretical models thermodynamics viral proteins x-ray crystallography

ALGGENTool Content

http://alggen.lsi.upc.es/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > cDNA, EST, SAGE
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

ALLGEN server provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.

NAR Web Server Issue 2003
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tagsalgorithms animals binding sites chickens chromosome mapping computational biology conserved sequence dna dna sequence analysis gene expression profiling genetic promoter regions genome genomics humans mice nucleic acid conformation nucleic acid databases nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology rats sequence alignment software design species specificity transcription factors x-ray crystallography

DHcLTool Content

http://sitron.bccs.uib.no/dhcl/

Protein > Domains and Motifs

DHcL provides analysis of the hierarchy of protein domain structures. DHcL detects closed loops and van der Waals locks, and outputs domain decomposition at different levels of protein domain structure hierarchy.

NAR Web Server Issue 2008
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tagsmolecular models statistical data interpretation tertiary protein structure x-ray crystallography

DIALTool Content

http://caps.ncbs.res.in/DIAL/home.html

Protein > 3-D Structure Prediction
Protein > Domains and Motifs

DIAL (Domain Identification Algorithm) is a web server for the automatic identification of structural domains given the three-dimensional coordinates of a protein.

NAR Web Server Issue 2005
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tagsalgorithms amino acid motifs amino acid sequence amino acids aspartic acid endopeptidases calmodulin chemical models cluster analysis database management systems documentation factual databases hydroxymethylbilane synthase molecular models molecular sequence data molecular structure papain porins protein conformation protein databases protein folding protein sequence analysis proteins reproducibility of results secondary protein structure sensitivity and specificity sequence alignment tertiary protein structure x-ray crystallography

DisEMBLTool Content

http://dis.embl.de/

Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction

A computational tool for prediction of disordered/unstructured regions within a protein sequence.

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tagscircular dichroism humans ligands magnetic resonance spectroscopy neural networks (computer) protein conformation proteins proteome sensitivity and specificity src homology domains statistics as topic temperature theoretical models ultraviolet rays x-ray crystallography

ElNemoTool Content

http://igs-server.cnrs-mrs.fr/elnemo/start.html

Protein > 3-D Structure Retrieval/Viewing
Protein > Molecular Dynamics and Docking

ElNemo (The Elastic Network Model) is a tool for predicting the possible movements (ie. conformational changes and other structural changes) of macromolecules. This tool allows users to compute, visualize, and analyse low-frequency normal modes of a protein.

NAR Web Server Issue 2004
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tagsmolecular models motion protein conformation proteins x-ray crystallography

FrogTool Content

http://bioserv.rpbs.jussieu.fr/cgi-bin/Frog

Other Molecules > Small Molecules

Frog (Free Online Drug Conformation) is a service aimed at generating 3D conformations for drug-like compounds starting from their 1D or 2D descriptions (smiles or sdf).

NAR Web Server Issue 2007
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tagsalgorithms chemical models chemistry computational biology computer simulation ligands molecular conformation molecular structure pharmaceutical chemistry pliability protein databases proteins quantitative structure-activity relationship x-ray crystallography

MODPROPEPTool Content

http://www.nii.res.in/~narendra/PROT_PEP_INTERACTION/index.html

Protein > 3-D Structure Prediction
Protein > Domains and Motifs

MODPROPEP is a server for structural modeling of protein kinases and MHC proteins in complex with their substrate peptides.

NAR Web Server Issue 2007
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tagsalgorithms animals computational biology computer simulation humans major histocompatibility complex peptides protein conformation protein databases proteins x-ray crystallography

oGNMTool Content

http://ignm.ccbb.pitt.edu/GNM_Online_Calculation.htm

Protein > Molecular Dynamics and Docking

Online Guassian Network Model (oGNM) calculates the equilibrium dynamics of any structure submitted in PDB format, using the Gaussian Network Model (GNM), a network model for representing biomolecules.

NAR Web Server Issue 2006
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tagsalgorithms binding sites chemical models computational biology computer simulation molecular models molecular structure motion normal distribution nucleic acid conformation oligonucleotides protein binding protein conformation protein databases protein folding protein sequence analysis proteins sequence alignment statistical models structure-activity relationship thermodynamics x-ray crystallography

PreBITool Content

http://pre-s.protein.osaka-u.ac.jp/prebi/

Protein > 3-D Structural Features

Prediction of Biological Interfaces (PreBI) is a server for predicting protein-protein interfaces in protein structures that maximizes both the degree of complementarity and the interface area.

NAR Web Server Issue 2006
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tagsdatabase management systems humans hydrophobic and hydrophilic interactions molecular models multiprotein complexes protein conformation protein databases proteins static electricity three-dimensional imaging x-ray crystallography

PROSESS: A Protein Structure Evaluation Suite and ServerTool Content

http://www.prosess.ca

Protein > 3-D Structure Prediction

PROSESS (PROtein Structure Evaluation Suite and Server) is a comprehensive web server designed to evaluate and validate protein structures generated by X-ray crystallography, NMR spectroscopy and computational modeling.

NAR Web Server Issue 2010
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tagsbiomolecular nuclear magnetic resonance molecular models protein conformation x-ray crystallography

ProtCIDDatabase Content

http://dunbrack2.fccc.edu/protcid

Protein > Databases

The protein common interface database (ProtCID) is a database that contains clusters of similar homodimeric and heterodimeric interfaces observed in multiple crystal forms (CFs). In ProtCID, protein chains in the protein data bank (PDB) are grouped based on their PFAM domain architectures. For a single PFAM architecture, all the dimers present in each CF are constructed and compared with those in other CFs that contain the same domain architecture. Interfaces occurring in two or more CFs comprise an interface cluster in the database. The same process is used to compare heterodimers of chains with different domain architectures. Our data therefore provide an independent check on publicly available annotations of the structures of biological interactions for PDB entries. Coordinates for all interfaces in a cluster are downloadable for further analysis.

This content is being maintained by dunbrack.

NAR Database Issue 2011
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tagsamino acid sequence homology dimerization molecular models phylogeny protein databases protein interaction domains and motifs protein interaction mapping proteins x-ray crystallography

ProteinCCDTool Content

http://xtal.nki.nl/ccd

DNA > Tools For the Bench
Expression > Protein Expression
Protein > Domains and Motifs
Protein > Protein Expression
Protein > Sequence Data
Protein > Sequence Features
Protein > Sequence Retrieval

Protein Crystallographic Construct Design (Protein CCD) is a meta-web server that facilitates the design of several truncated constructs of a protein using experimental data or sequence analysis tools. From input DNA sequence, information on disorder, coiled coils, transmembrane segments, domains and domain linkers are collected from secondary structure prediction servers. Users can select starts and ends for protein constructs and ProteinCCD wil design suitable PCR primers.

NAR Web Server Issue 2009
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tagsamino acid sequence dna sequence analysis oligonucleotides polymerase chain reaction protein sequence analysis proteins secondary protein structure sequence deletion tertiary protein structure x-ray crystallography

ProtemotTool Content

http://protemot.csbb.ntu.edu.tw/

Protein > 3-D Structural Features

The Protein motif (Protemot) server predicts protein binding sites based on structural templates automatically extracted from crystal structures of protein-ligand complexes in the PDB.

NAR Web Server Issue 2006
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tagsbinding sites ligands molecular models protein databases protein structural homology proteins tertiary protein structure x-ray crystallography

PTGLDatabase Content

http://ptgl.zib.de

Protein > Databases

Protein Topology Graph Library (PTGL) is a database on protein secondary structure topologies, including search facilities, the visualization as intuitive topology diagrams as well as in the 3D structure, and additional information. Secondary structure-based protein topologies are represented uniquely as undirected labeled graphs in four different ways allowing for exploration under different aspects. The linear notations, and the 2D and 3D diagrams of each notation facilitate a deeper understanding of protein topologies. Several search functions for topologies and sub-topologies, BLAST search possibility, and links to SCOP, CATH and PDBsum support individual and large-scale investigation of protein structures. Main structural patterns for common structural motifs like TIM-barrel or Jelly Roll are pre-implemented, and can easily be searched.

NAR Database Issue 2010
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tagsamino acid motifs animals computational biology genetic databases humans protein conformation protein databases proteins secondary protein structure x-ray crystallography