IBIS

Names
More detailed information about this field from each metasource.

IBIS
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:57.925400

ibis_ncbi
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:57.925400

Other names: ibis_ncbi

Inferred Biomolecular Interaction Server: protein-protein, ligand- and nucleic acid-binding sites

Webpage:

http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi

Publications:

Publications
More detailed information about this field from each metasource.

Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites
PMID: 19843613
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:57.925400

http://dx.doi.org/10.1093/nar/GKR997
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites PubMed citations: 52.

52 articles citing: Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites

A Deep Learning and XGBoost-Based Method for Predicting Protein-Protein Interaction Sites. PMID:34764983
In silico Approaches for the Design and Optimization of Interfering Peptides Against Protein-Protein Interactions. PMID:33996914
Pharmacological and molecular dynamics analyses of differences in inhibitor binding to human and nematode PDE4: Implications for management of parasitic nematodes. PMID:30917179
In Silico Analysis of Homologous Heterodimers of Cruzipain-Chagasin from Structural Models Built by Homology. PMID:30875920
Ranking Enzyme Structures in the PDB by Bound Ligand Similarity to Biological Substrates. PMID:29551288
Exploring the potential of 3D Zernike descriptors and SVM for protein-protein interface prediction. PMID:29409446
Exploring Protein-Protein Interactions as Drug Targets for Anti-cancer Therapy with In Silico Workflows. PMID:28809006
Annotating Mutational Effects on Proteins and Protein Interactions: Designing Novel and Revisiting Existing Protocols. PMID:28188534
Elucidating the druggable interface of protein-protein interactions using fragment docking and coevolutionary analysis. PMID:27911825
Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies. PMID:26585402
Mutations in the KDM5C ARID Domain and Their Plausible Association with Syndromic Claes-Jensen-Type Disease. PMID:26580603
Improving protein-ligand docking with flexible interfacial water molecules using SWRosettaLigand. PMID:26515196
Understanding the fabric of protein crystals: computational classification of biological interfaces and crystal contacts. PMID:26508758
A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces. PMID:26485003
Computational prediction of protein interfaces: A review of data driven methods. PMID:26460190
Structural Perspectives on the Evolutionary Expansion of Unique Protein-Protein Binding Sites. PMID:26213149
Surfing the Protein-Protein Interaction Surface Using Docking Methods: Application to the Design of PPI Inhibitors. PMID:26111183
Progress and challenges in predicting protein interfaces. PMID:25971595
Dissecting the calcium-induced differentiation of human primary keratinocytes stem cells by integrative and structural network analyses. PMID:25946651
Algorithmic approaches to protein-protein interaction site prediction. PMID:25713596
Coverage of protein domain families with structural protein-protein interactions: current progress and future trends. PMID:24931138
Computational large-scale mapping of protein-protein interactions using structural complexes. PMID:24510594
PeptiSite: a structural database of peptide binding sites in 4D. PMID:24406170
Cancer missense mutations alter binding properties of proteins and their interaction networks. PMID:23799087
Characterizing protein domain associations by Small-molecule ligand binding. PMID:23745168
Correlating protein hot spot surface analysis using ProBiS with simulated free energies of protein-protein interfacial residues. PMID:23009716
Exploring the evolution of protein function in Archaea. PMID:22646318
Annotation of functional sites with the Conserved Domain Database. PMID:22434827
Predicting protein-protein interface residues using local surface structural similarity. PMID:22424103
Homology inference of protein-protein interactions via conserved binding sites. PMID:22303436
SPPS: a sequence-based method for predicting probability of protein-protein interaction partners. PMID:22292078
Large-scale mapping of human protein interactome using structural complexes. PMID:22261719
Modulating protein-protein interactions with small molecules: the importance of binding hotspots. PMID:22198293
MMDB: 3D structures and macromolecular interactions. PMID:22135289
IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins. PMID:22102591
Pocketome: an encyclopedia of small-molecule binding sites in 4D. PMID:22080553
InterEvol database: exploring the structure and evolution of protein complex interfaces. PMID:22053089
SCOWLP update: 3D classification of protein-protein, -peptide, -saccharide and -nucleic acid interactions, and structure-based binding inferences across folds. PMID:21992011
HomPPI: a class of sequence homology based protein-protein interface prediction methods. PMID:21682895
SA-Mot: a web server for the identification of motifs of interest extracted from protein loops. PMID:21665924
Tumor-targeted RNA-interference: functional non-viral nanovectors. PMID:21572539
Caught in self-interaction: evolutionary and functional mechanisms of protein homooligomerization. PMID:21572178
Database resources of the National Center for Biotechnology Information. PMID:21097890
DIMA 3.0: Domain Interaction Map. PMID:21097782
BISC: binary subcomplexes in proteins database. PMID:21081561
Mechanisms of protein oligomerization, the critical role of insertions and deletions in maintaining different oligomeric states. PMID:21048085
The protein common interface database (ProtCID)--a comprehensive database of interactions of homologous proteins in multiple crystal forms. PMID:21036862
Mutational dynamics of murine angiogenin duplicates. PMID:20950426
Knowledge-based annotation of small molecule binding sites in proteins. PMID:20594344
Functional states of homooligomers: insights from the evolution of glycosyltransferases. PMID:20381499
ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder. PMID:19906708
Evolution of protein binding modes in homooligomers. PMID:19879880
http://dx.doi.org/10.1093/nar/GKR997

Tags:

Tags
More detailed information about this field from each metasource.

metabolic and signaling pathways
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

protein-protein interactions
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

protein binding sites
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:57.925400

molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:57.925400

protein interactions
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:57.925400

small molecules
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:57.925400

nucleic acid sites, features and motifs
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:57.925400

metabolic and signaling pathways protein-protein interactions protein binding sites molecular interactions, pathways and networks protein interaction small molecule nucleic acid sites, features and motifs

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BIND: The Biomolecular Interaction Network Db

LigAsite

Pocketome: an encyclopedia of small-molecule binding sites in 4D

Pocket Similarity Search using Multiple-Sketches

Human Protein-Protein Interaction rEference

Binding MOAD

SuperSite

ProNAB

TRIP

AtPID

Dockground

PDZBase

PIPs

HitPredict

RegPrecise

BioCarta Pathways

Nucleic Acids Database

Protein Interaction Network Analysis platform

PAIR

Bacterial Protein Interaction Database