Related references
Note: Only part of the references are listed.Identifying protein-protein interface via a novel multi-scale local sequence and structural representation
Fei Guo et al.
BMC BIOINFORMATICS (2019)
Protein-protein binding supersites
Raji Viswanathan et al.
PLOS COMPUTATIONAL BIOLOGY (2019)
Prediction of Protein-Peptide Interactions with a Nearest Neighbor Algorithm
Bi-Qing Li et al.
CURRENT BIOINFORMATICS (2018)
Machine Learning Approaches for Protein-Protein Interaction Hot Spot Prediction: Progress and Comparative Assessment
Siyu Liu et al.
MOLECULES (2018)
Protein-protein interaction specificity is captured by contact preferences and interface composition
Francesca Nadalin et al.
BIOINFORMATICS (2018)
DeepInteract: Deep Neural Network Based Protein-Protein Interaction Prediction Tool
Sunil Patel et al.
CURRENT BIOINFORMATICS (2017)
Improved prediction of protein-protein interactions using novel negative samples, features, and an ensemble classifier
Leyi Wei et al.
ARTIFICIAL INTELLIGENCE IN MEDICINE (2017)
Computational modeling of protein assemblies
Neelesh Soni et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2017)
Progress and challenges in predicting protein interfaces
Reyhaneh Esmaielbeiki et al.
BRIEFINGS IN BIOINFORMATICS (2016)
FRODOCK 2.0: fast protein-protein docking server
Erney Ramirez-Aportela et al.
BIOINFORMATICS (2016)
Protein-protein interface prediction based on hexagon structure similarity
Fei Guo et al.
COMPUTATIONAL BIOLOGY AND CHEMISTRY (2016)
Algorithmic approaches to protein-protein interaction site prediction
Tristan T. Aumentado-Armstrong et al.
ALGORITHMS FOR MOLECULAR BIOLOGY (2015)
DOCKSCORE: a webserver for ranking protein-protein docked poses
Sony Malhotra et al.
BMC BIOINFORMATICS (2015)
Structural neighboring property for identifying protein-protein binding sites
Fei Guo et al.
BMC SYSTEMS BIOLOGY (2015)
Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution
Xiaojun Xu et al.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2015)
CCharPPI web server: computational characterization of protein-protein interactions from structure
Iain H. Moal et al.
BIOINFORMATICS (2015)
Application of Enhanced Sampling Monte Carlo Methods for High-Resolution Protein-Protein Docking in Rosetta
Zhe Zhang et al.
PLOS ONE (2015)
PPCheck: A Webserver for the Quantitative Analysis of Protein-Protein Interfaces and Prediction of Residue Hotspots
Anshul Sukhwal et al.
BIOINFORMATICS AND BIOLOGY INSIGHTS (2015)
Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis
Philipp Blohm et al.
NUCLEIC ACIDS RESEARCH (2014)
Scoring functions for protein-protein interactions
Iain H. Moal et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2013)
Oligomerisation status and evolutionary conservation of interfaces of protein structural domain superfamilies
Anshul Sukhwal et al.
MOLECULAR BIOSYSTEMS (2013)
Expanding the frontiers of protein-protein modeling: From docking and scoring to binding affinity predictions and other challenges
Chiara Pallara et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2013)
A Markov-chain model description of binding funnels to enhance the ranking of docked solutions
Mieczyslaw Torchala et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2013)
CD-HIT: accelerated for clustering the next-generation sequencing data
Limin Fu et al.
BIOINFORMATICS (2012)
DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking
Shiyong Liu et al.
BMC BIOINFORMATICS (2011)
Scoring by Intermolecular Pairwise Propensities of Exposed Residues (SIPPER): A New Efficient Potential for Protein-Protein Docking
Carles Pons et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)
Using Correlated Parameters for Improved Ranking of Protein-Protein Docking Decoys
Pralay Mitra et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)
PROCOS: Computational Analysis of Protein-Protein Complexes
Florian Fink et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)
A Collaborative Filtering Approach for Protein-Protein Docking Scoring Functions
Thomas Bourquard et al.
PLOS ONE (2011)
On the analysis of protein-protein interactions via knowledge-based potentials for the prediction of protein-protein docking
Elisenda Feliu et al.
PROTEIN SCIENCE (2011)
Evidence for Network Evolution in an Arabidopsis Interactome Map
Pascal Braun et al.
SCIENCE (2011)
LIBSVM: A Library for Support Vector Machines
Chih-Chung Chang et al.
ACM TRANSACTIONS ON INTELLIGENT SYSTEMS AND TECHNOLOGY (2011)
Crystal Contacts as Nature's Docking Solutions
Evgeny Krissinel
JOURNAL OF COMPUTATIONAL CHEMISTRY (2010)
Are Scoring Functions in Protein-Protein Docking Ready To Predict Interactomes? Clues from a Novel Binding Affinity Benchmark
Panagiotis L. Kastritis et al.
JOURNAL OF PROTEOME RESEARCH (2010)
The Negatome database: a reference set of non-interacting protein pairs
Pawel Smialowski et al.
NUCLEIC ACIDS RESEARCH (2010)
Predicting protein complex geometries with a neural network
Myong-Ho Chae et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)
Fiber Dock: Flexible induced-fit backbone refinement in molecular docking
Efrat Mashiach et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)
A survey of available tools and web servers for analysis of protein-protein interactions and interfaces
Nurcan Tuncbag et al.
BRIEFINGS IN BIOINFORMATICS (2009)
Human Protein Reference Database-2009 update
T. S. Keshava Prasad et al.
NUCLEIC ACIDS RESEARCH (2009)
Proteome Organization in a Genome-Reduced Bacterium
Sebastian Kuehner et al.
SCIENCE (2009)
How proteins get in touch: Interface prediction in the study of biomolecular complexes
Sjoerd J. de Vries et al.
CURRENT PROTEIN & PEPTIDE SCIENCE (2008)
The RosettaDock server for local proteinprotein docking
Sergey Lyskov et al.
NUCLEIC ACIDS RESEARCH (2008)
A combination of rescoring and refinement significantly improves protein docking performance
Brian Pierce et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2008)
An iterative knowledge-based scoring function for protein-protein recognition
Sheng-You Huang et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2008)
High-quality binary protein interaction map of the yeast interactome network
Haiyuan Yu et al.
SCIENCE (2008)
An in vivo map of the yeast protein interactome
Kirill Tarassov et al.
SCIENCE (2008)
A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys
Shide Liang et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2007)
FireDock: Fast interaction refinement in molecular docking
Nelly Andrusier et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2007)
Inference of macromolecular assemblies from crystalline state
Evgeny Krissinel et al.
JOURNAL OF MOLECULAR BIOLOGY (2007)
Protein docking using surface matching and supervised machine learning
Andrew J. Bordner et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2007)
pyDock: Electrostatics and desolvation for effective scoring of rigid-body protein-protein docking
Tammy Man-Kuang Cheng et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2007)
ZRANK: Reranking protein docking predictions with an optimized energy function
Brian Pierce et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2007)
Specificity in protein interactions and its relationship with sequence diversity and coevolution
Luke Hakes et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
PIER: Protein interface recognition for structural proteomics
Irina Kufareva et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2007)
A protein-specifically adapted scoring function for the reranking of docking solutions
Wolfgang Mueller et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2007)
A new protein-protein docking scoring function based on interface residue properties
J. Bernauer et al.
BIOINFORMATICS (2007)
Large-scale mapping of human protein-protein interactions by mass spectrometry
Rob M. Ewing et al.
MOLECULAR SYSTEMS BIOLOGY (2007)
MINT: the molecular INTeraction database
Andrew Chatr-aryamontri et al.
NUCLEIC ACIDS RESEARCH (2007)
IntAct - open source resource for molecular interaction data
S. Kerrien et al.
NUCLEIC ACIDS RESEARCH (2007)
Intramolecular surface contacts contain information about protein-protein interface regions
Sjoerd J. de Vries et al.
BIOINFORMATICS (2006)
An algorithm for predicting protein-protein interaction sites: Abnormally exposed amino acid residues and secondary structure elements
J Hoskins et al.
PROTEIN SCIENCE (2006)
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
NJ Krogan et al.
NATURE (2006)
Towards a proteome-scale map of the human protein-protein interaction network
JF Rual et al.
NATURE (2005)
A human protein-protein interaction network:: A resource for annotating the proteome
U Stelzl et al.
CELL (2005)
Development and testing of an automated approach to protein docking
A Tovchigrechko et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)
PatchDock and SymmDock: servers for rigid and symmetric docking
D Schneidman-Duhovny et al.
NUCLEIC ACIDS RESEARCH (2005)
Cation-π interactions in protein-protein interfaces
PB Crowley et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)
Interaction network containing conserved and essential protein complexes in Escherichia coli
G Butland et al.
NATURE (2005)
A map of the interactome network of the metazoan C-elegans
SM Li et al.
SCIENCE (2004)
The Database of Interacting Proteins: 2004 update
L Salwinski et al.
NUCLEIC ACIDS RESEARCH (2004)
A protein interaction map of Drosophila melanogaster
L Giot et al.
SCIENCE (2003)
Dissecting subunit interfaces in homodimeric proteins
RP Bahadur et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2003)
The relationship between sequence and interaction divergence in proteins
P Aloy et al.
JOURNAL OF MOLECULAR BIOLOGY (2003)
Protein-protein docking with a reduced protein model accounting for side-chain flexibility
M Zacharias
PROTEIN SCIENCE (2003)
HADDOCK: A protein-protein docking approach based on biochemical or biophysical information
C Dominguez et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)
Analysing six types of protein-protein interfaces
Y Ofran et al.
JOURNAL OF MOLECULAR BIOLOGY (2003)
Combination of scoring functions improves discrimination in protein-protein docking
J Murphy et al.
PROTEINS-STRUCTURE FUNCTION AND GENETICS (2003)
Dissecting protein-protein recognition sites
P Chakrabarti et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2002)
A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
P Uetz et al.
NATURE (2000)
The Protein Data Bank
HM Berman et al.
NUCLEIC ACIDS RESEARCH (2000)