MultiBind statistics

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Citations per year

Number of citations per year for the bioinformatics software tool MultiBind
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Tool usage distribution map

This map represents all the scientific publications referring to MultiBind per scientific context
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Protocols

MultiBind specifications

Information


Unique identifier OMICS_23985
Name MultiBind
Alternative name Multiple Alignment of Protein Binding Sites
Software type Application/Script
Interface Web user interface
Restrictions to use None
Input data A PDB code or a file with complexes' structures.
Input format PDB, ZIP
Output data A set of physico-chemical properties.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Haim Wolfson

Information


Unique identifier OMICS_23985
Name MultiBind
Alternative name Multiple Alignment of Protein Binding Sites
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


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Maintainer


  • person_outline Haim Wolfson

Publications for Multiple Alignment of Protein Binding Sites

MultiBind citations

 (11)
library_books

Normal Modes Expose Active Sites in Enzymes

2016
PLoS Comput Biol
PMCID: 5225006
PMID: 28002427
DOI: 10.1371/journal.pcbi.1005293

[…] rs of ligand binding sites have also been constructed and may be used to infer unknown ligand binding sites based on homology and other attributes such as Pocketome [], FunFold [], scPDB [], IBIS [], Multibind [], fPop [], and FINDSITE []. To date however, no comprehensive study comparing geometry based techniques has been performed.Normal-mode analysis is one of the standard techniques for studyi […]

library_books

Modeling enzyme ligand binding in drug discovery

2015
J Cheminform
PMCID: 4594084
PMID: 26457119
DOI: 10.1186/s13321-015-0096-0

[…] pair exhibited different folds but had known similar binding sites and performed a similar function. ProBiS was compared to three different structural alignment algorithms; DaliLite [], MolLoc [] and MultiBind []. The comparison between the methods was made by calculating the RMSD between previously identified, similar binding site residues, after the proteins in the pair have been superimposed. P […]

call_split

Similarities between the Binding Sites of SB 206553 at Serotonin Type 2 and Alpha7 Acetylcholine Nicotinic Receptors: Rationale for Its Polypharmacological Profile

2015
PLoS One
PMCID: 4526571
PMID: 26244344
DOI: 10.1371/journal.pone.0134444
call_split See protocol

[…] Structural alignments of the binding sites of SB-206553 at the 5-HT2 and α7 nACh receptors were performed using the MultiBind computational method []. This approach reveals the common physicochemical patterns that may be responsible for the binding of the same ligand to different protein targets. For the recognitio […]

library_books

Exploration of binding site pattern in arachidonic acid metabolizing enzymes, Cyclooxygenases and Lipoxygenases

2015
BMC Res Notes
PMCID: 4416244
PMID: 25886468
DOI: 10.1186/s13104-015-1101-4

[…] er, COX-1 and COX-2 are members of the same family and they share large similarity with each other in their enzyme reaction with their common substrate AA. Pairwise alignments of the binding sites in MultiBind showed that they have great similarity at the AA binding site. They were scored 90.4106 with 36 similar features. The most common features observed were aliphatic (ALI) and aromatic pi conta […]

library_books

Space related pharma motifs for fast search of protein binding motifs and polypharmacological targets

2012
BMC Genomics
PMCID: 3521469
PMID: 23281852
DOI: 10.1186/1471-2164-13-S7-S21

[…] structures, protein structures have been proposed to analyze the structural motifs and to describe the binding environment [,]. Most of these studies (e.g. SPASM [], Superimpose [], RASMOT-3D PRO [], MultiBind [], and Wu et al. []) search the similar local structures or binding sites (active sites) based on only one structural motif. However, a protein-ligand binding interface usually consists of […]

library_books

Protein Surface Matching by Combining Local and Global Geometric Information

2012
PLoS One
PMCID: 3398928
PMID: 22815760
DOI: 10.1371/journal.pone.0040540

[…] ng down on runtime for pairwise comparisons. The reported running time for sup-CK ranges from 0.2 and 1.3 seconds per comparison when running on a machine with a 2.5 GHz CPU. While timing results for MultiBind were not reported for these data sets, reports run times ranging between 8 and 58 minutes for multiple alignments of groups of 5 binding sites when utilizing an Intel Pentium IV 2.60 GHz pr […]


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MultiBind institution(s)
School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel; Physical Biosciences Division, Berkeley National Lab, CA, USA; Sackler Inst. of Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Basic Research Program, SAIC-Frederick, Inc., Laboratory of Experimental and Computational Biology, NCI-Frederick, Frederick, MD, USA
MultiBind funding source(s)
Supported by the Clore PhD Fellowship, the Israel Science Foundation (grant no. 281/05), the NIAID, NIH (grant No. 1UC1AI067231), the Binational US-Israel Science Foundation (BSF) and the Hermann Minkowski-Minerva Center for Geometry.

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