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Welcome to the Made In Weizmann Portal
A single entry point for Databases, FTP Servers, On-line Data Processing engines and Software designed and developed at the Weizmann Institute of Science, Rehovot, Israel.
1st Made In Weizmann Conference
26th January 2011
Schmidt Lecture Hall
Dr. Jaime Prilusky

OCA facilitates the understanding of the genomics/proteomics biological data through data analysis and synthesis. The data integration process brings together dispersed pieces of information, generating comprehensive summaries that might be just what a researcher needs for crystallizing an idea or understanding a problem.
Marilyn Safran, M.Sc.

GeneCards is a database of human genes, their products and their involvement in diseases. It offers concise information about the functions of all human genes that have an approved symbol, as well as selected others.
Dr. Jaime Prilusky

A single entry point for Databases, Software, FTP servers and On-line data processing engines designed and developed at the Weizmann Institute of Science, Rehovot, Israel.
Eran Eyal, M.Sc.

A database and analysis tool for structural affects of point mutations
Dr. Vered Chalifa-Caspi

A system for annotation of Affymetrix oligunucleotide arrays, with links to GeneCards and other databases.
Dr. Tsviya Olender

A database of human olfactory receptos, the largest gene family in multi-cellular organisms. A set of specialized features supply a global overview of their evolution and function, including information on the phylogenetic relationship to olfactory receptors from other mammalian species.
PDB Records Name
Dr. Jaime Prilusky

Distribution of Records in PDB files (indispensable for extracting data from multiple PDB files)
Dr. Jaime Prilusky
Eran Hodis, M.Sc.
Prof. Joel Sussman

Proteopedia is a wiki-like interactive database to collect, organize and disseminate structural and functional knowledge about protein, RNA, DNA, and other macromolecules, and their assemblies and interactions with small molecules, in a manner that is relevant and broadly accessible to students and scientists.
On-line Data Processing
Dr. Vladimir Sobolev
Prof. Meir Edelman
Dr. Jaime Prilusky

Ligand-Protein Contacts & Contacts of Structural Units
Dr. Clifford Felder
Prof. Joel Sussman

With this server you can discover if your protein might have an unusally large net charge or dipole moment, and how this might relate to specific structural features of the protein, and thereby its function.
Correlated Mutations
Itamar Kass, M.Sc.
Prof. Amnon Horovitz

Analysis of correlated mutations
Predicting Association Rate Enhancement (PARE)
Prof. Gideon Schreiber

The program PARE calculates the change in rate of association (kon) of mutant protein-protein interaction complexes from the change in the Debye Huckel energy of interaction between proteins using transition state theory. As input, the pdb coordinates of the complex are required. For calculating absolute rates, one has to add the value of kon of the wild-type complex as well.
FSSP to CATH and SCOP server (F2CS)
Prof. Eytan Domany
Gaddy Getz, M.Sc.

The F2CS server provides access to the software, F2CS2.00, that implements an automated prediction server of SCOP's class and fold classifications and CATH's class, architechture and topology classifications for any protein that appears in the latest version of the FSSP database (Getz et al., Proteins (2002) 46, 405). The prediction is based on the FSSP Z-scores.
Coupled Two-Way Clustering server (CTWC)
Prof. Eytan Domany
Gaddy Getz, M.Sc.

The CTWC server provides access to the software, CTWC1.00, that implements Coupled Two Way Clustering [Getz et al., PNAS (2000), 97, 12079], a method designed to mine gene expression data. The user uploads the expression matrix and, optionally, a table of labels for samples and one for genes. CTWC clusters groups of samples, using their expression over groups of genes, and vice versa.
Dr. Jaime Prilusky

A tool for sequence identification, analysis, characterization and annotation. This server will try to find relevant information related to your sequence.
Dr. Jaime Prilusky
Dr. Clifford Felder
Prof. Joel Sussman

Will this protein fold? This dynamic interactive process estimates the local and general probability, based on algorithm proposed by Uversky VN, Gillespie JR, and Fink AL. Why are 'natively unfolded' proteins unstructured under physiologic conditions? Proteins 2000; 41:415-427.
Motif Analysis Workbench
Michal Lapidot, M.Sc.
Dr. Tzachi Pilpel

The Motif Analysis Workbench is a WWW interface for automated comprehensive analyses of promoter regulatory motifs and the effect they exert on mRNA expression profiles.
Prof. Gad Yagil

A program to map oligopurine.oligopyrimidine and other binary DNA tracts. Also, a short one line description for each gene in a chromosome.
Dr. Jaime Prilusky

BestPrimers(c) provides a simple interface for primers calculation, with FoldIndex(c) support.
Dr. Jaime Prilusky

SeqAlert(c) is a sequence alerting service that will periodically compare your sequence(s) against sequences from determined 3D structures, or structures being determined at PDB and TargetDB, the database of target sequences from worldwide structural genomics projects.
Dr. Jaime Prilusky

RecentReferences will try to find recent publications related to your DNA or protein sequence.
Eran Eyal, M.Sc.

Prediction of side chain conformations and mutations on fixed backbone
Eran Eyal, M.Sc.

Analysis of two spheres of contacting residues around ligands (using LPC and CSU)
Prof. Gideon Schreiber
Hani Neuvirth, M.Sc.

Given a PDB structure of an unbound protein ProMate predicts the location of a potential binding site where transient interaction with another protein may occur.
Dr. Jaime Prilusky

Suggest an Expression System based on a provided sequence. How: suggestES takes the protein sequence you provide and scans a large database with protein sequences with known results for different expression systems.
Dr. Jaime Prilusky

verifyCloning compares your source data with one or more results from DNA sequencing.
Yosef Shaul, M.Sc.
Prof. Gideon Schreiber
Dr. Jaime Prilusky

HyPare is a newly designed tool based on the PARE algorithm (Predicting Association Rate Enhancement). With HyPare you can find hotspots for association, and thus, engineer your proteins for faster and tighter binding.
NUMODs motifs finder
Einat Sitbon, M.Sc.

NUMODs (nuclease-associated modular DNA-binding domains) can be found, in addition to a service that locates NUMODs on a given protein/DNA sequence. NUMODs are new types of short conserved sequence domains in homing endonucleases and related proteins. These domains are modular, appearing in various combinations. One domain includes a motif known by structure as a novel sequence-specific DNA-binding helix. Sequence similarity shows two other domains to be new types of HTH DNA-binding domains. We term the new domains nuclease-associated modular DNA-binding domains (NUMODs).
Dr. Shmuel Pietrokovski
Arye Shemesh, B.Sc.
Dr. Gil Amitai
Einat Sitbon, M.Sc.

Enables the identification of active sites in enzymes based on the analysis of protein structures as networks of interactions between amino acids. The network property of closeness describes the average shortest path of each residue in a given protein structure from all other residues within the structure. The combination of high closeness values and relative surface area of each residue enables to predict its likelihood of being an active site residue. The optimal values of closeness and relative surface area were derived from a thorough examination of 178 protein structures with well annotated active sites (Bartlett GJ. et al. J Mol Biol. 2002 Nov 15;324(1):105-21).
Ilan Volovitz, M.Sc.
Prof. Lea Eisenbach

The program determines which of all possible peptide nonamers from a protein sequence adheres to a mouse MHC class-II molecule. All motifs used are experimentally derived.
Dr. Ofer Rahat
Dr. Jaime Prilusky
Dr. Yaakov Levy
Dr. Barak Raveh
Dr. Uri Alon
Prof. Gideon Schreiber

a PROTeins MOTif analysis tool. This web site analyzes structure of proteins and output the list of hydrogen bonding patterns network motifs.
Prof. Gideon Schreiber
Dr. Dana Reichmann

AquaProt analyses protein-protein binding interface, defines inter-residue interaction map within the interface and extracts related water molecules.
Prof. Gideon Schreiber

Hunter is a knowledge-based potential for protein structure modeling and evaluation. It is based on a novel 4-distance description of side chain interactions. This web site interactively presents Jmol visualization depicting preferred orientation of two residues in 3D and 2D space, a tool predict side chain conformations and changes in protein stability and binding affinity upon mutation.
Noam Leviatan, M.Sc.
Prof. Robert Fluhr

Plant hormones play a pivotal role in plant growth and physiology. HORMONOMETER is a tool for evaluating any Arabidopsis transcriptome response through the perspective of similar events that happen upon direct hormonal activation. This tool applies vector-base analysis to rapidly compare lists of user supplied transcripts activity based on microarray to a database of hormone transcript profiles yielding correlation values and a color coded heat map.
Dr. Lester Shulman
Dr. Jaime Prilusky

(Nucleotide Identity Comparisons for Evolution and Recombination) allows evaluation of the quality of inferred phylogenies (evolutionary trees).
Dr. Jaime Prilusky

Bio::Maxd provides methods for uploading and retrieving data to/from a maxd (MySQL) database.
Dr. Jaime Prilusky

A complete framework for managing and publishing activities (Workshops, Conferences, Courses) and dealing with registrations to lectures and practices.
Dr. Miriam Eisenstein
Noga Kowalsman, M.Sc.

MolFit is a protein-protein docking program, which uses grid representations of the docked molecules and FFT to calculate the correlation between the representations. MolFit was very successful in the recent CAPRI blind docking prediction tests. The program can be downloaded from our site.
Ron Milo, M.Sc.
Shalev Itzkovitz, M.Sc.
Nadav Kashtan, M.Sc.
Dr. Uri Alon

Network Motifs detection software. Enumerates all n-node connected subgraphs (n=3,4,5...) and compares their counts to random networks with the same degree sequences. Detects Network Motifs - subgraphs which appear in the network in significantly higher numbers than in the random networks.
Dr. Jaime Prilusky

PassportŠ is a small application to ease the process of opening a secure channel to the WIS, by authenticating yourself to the Firewall server.
Ofra Golani
Dr. Meirav Galun
Dr. Ronen Basri
Dr. Ida Rishal
Prof. Michael Fainzilber

Neurite length and morphology analysis of fluorescent microscopy images of nerve cells.
Ofra Golani
Dr. Meirav Galun
Dr. Ronen Basri
Dr. Suha Naffar Abu-Amara
Prof. Benny Geiger

Quantitative analysis of high throughput cell migration assay. The cell migration assay is based on a modified Phagokinetic tracks procedure, in which motile cells "leave their tracks" on a specialized surface
Ofra Golani
Dr. Hagit Dafni
Reut Avni, M.Sc.
Prof. Michal Neeman

Analysis and Visualization of MRI data

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Server by Jaime Prilusky, 2002,2010
Bioinformatics and Biological Computing
Weizmann Institute of Science