Prediction of protein binding sites and hot spots (Q58428610)

Identification of protein oligomerization states by analysis of interface conservation

21 January 2018

1 reference

Conservation helps to identify biologically relevant crystal contacts.

21 January 2018

1 reference

NOXclass: prediction of protein-protein interaction types

21 January 2018

1 reference

PQS: a protein quaternary structure file server.

21 January 2018

1 reference

ProtBuD: a database of biological unit structures of protein families and superfamilies.

21 January 2018

1 reference

Using protein binding site prediction to improve protein docking

21 January 2018

1 reference

Prediction of protein-protein interactions by docking methods.

21 January 2018

1 reference

Flexible protein-protein docking

21 January 2018

1 reference

High-resolution protein-protein docking

21 January 2018

1 reference

Recent Progress and Future Directions in Protein-Protein Docking

21 January 2018

1 reference

Modelling protein docking using shape complementarity, electrostatics and biochemical information

21 January 2018

1 reference

A novel shape complementarity scoring function for protein‐protein docking

21 January 2018

1 reference

Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques

21 January 2018

1 reference

PatchDock and SymmDock: servers for rigid and symmetric docking

21 January 2018

1 reference

Soft protein-protein docking in internal coordinates

21 January 2018

1 reference

HADDOCK: a protein-protein docking approach based on biochemical or biophysical information

21 January 2018

1 reference

Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations

21 January 2018

1 reference

pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking

21 January 2018

1 reference

Successful discrimination of protein interactions.

21 January 2018

1 reference

Modeling side-chains using molecular dynamics improve recognition of binding region in CAPRI targets.

21 January 2018

1 reference

A role for surface hydrophobicity in protein-protein recognition

21 January 2018

1 reference

Protein-protein interactions: a review of protein dimer structures

21 January 2018

1 reference

Prediction of protein-protein interaction sites using patch analysis.

21 January 2018

1 reference

Analysis of protein-protein interaction sites using surface patches

21 January 2018

1 reference

Principles of protein-protein recognition

21 January 2018

1 reference

The atomic structure of protein-protein recognition sites

21 January 2018

1 reference

On the role of electrostatic interactions in the design of protein-protein interfaces

21 January 2018

1 reference

A simple definition of structural regions in proteins and its use in analyzing interface evolution.

21 January 2018

1 reference

Anchor residues in protein-protein interactions

21 January 2018

1 reference

Restricted mobility of conserved residues in protein-protein interfaces in molecular simulations.

21 January 2018

1 reference

Comparing interfacial dynamics in protein-protein complexes: an elastic network approach

21 January 2018

1 reference

The origin of allosteric functional modulation: multiple pre-existing pathways

21 January 2018

1 reference

Transient protein-protein interactions: structural, functional, and network properties

21 January 2018

1 reference

Dynamic interactions of proteins in complex networks: a more structured view.

21 January 2018

1 reference

iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence

21 January 2018

1 reference

Towards inferring time dimensionality in protein-protein interaction networks by integrating structures: the p53 example

21 January 2018

1 reference

Principles of protein-protein interactions

21 January 2018

1 reference

Analysing six types of protein-protein interfaces

21 January 2018

1 reference

Diversity of protein-protein interactions

21 January 2018

1 reference

The many faces of protein-protein interactions: A compendium of interface geometry

21 January 2018

1 reference

In silico prediction of binding sites on proteins

21 January 2018

1 reference

How proteins get in touch: interface prediction in the study of biomolecular complexes.

21 January 2018

1 reference

Progress and challenges in predicting protein-protein interaction sites

21 January 2018

1 reference

A survey of available tools and web servers for analysis of protein-protein interactions and interfaces

21 January 2018

1 reference

ISIS: interaction sites identified from sequence.

21 January 2018

1 reference

TreeDet: a web server to explore sequence space

21 January 2018

1 reference

ProMate: a structure based prediction program to identify the location of protein-protein binding sites

21 January 2018

1 reference

Protein binding site prediction using an empirical scoring function

21 January 2018

1 reference

InterProSurf: a web server for predicting interacting sites on protein surfaces

21 January 2018

1 reference

PRISM: protein interactions by structural matching

21 January 2018

1 reference

ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information

21 January 2018

1 reference

ET viewer: an application for predicting and visualizing functional sites in protein structures

21 January 2018

1 reference

Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling

21 January 2018

1 reference

WHISCY: what information does surface conservation yield? Application to data-driven docking.

21 January 2018

1 reference

PIER: protein interface recognition for structural proteomics.

21 January 2018

1 reference

Recognition of functional sites in protein structures.

21 January 2018

1 reference

Improved prediction of protein-protein binding sites using a support vector machines approach.

21 January 2018

1 reference

Prediction of protein interaction sites from sequence profile and residue neighbor list.

21 January 2018

1 reference

Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data

21 January 2018

1 reference

Prediction-based fingerprints of protein-protein interactions.

21 January 2018

1 reference

Annotating nucleic acid-binding function based on protein structure.

21 January 2018

1 reference

meta-PPISP: a meta web server for protein-protein interaction site prediction.

21 January 2018

1 reference

PI2PE: protein interface/interior prediction engine

21 January 2018

1 reference

SHARP2: protein-protein interaction predictions using patch analysis.

21 January 2018

1 reference

Optimal docking area: a new method for predicting protein-protein interaction sites

21 January 2018

1 reference

Identification of protein-protein interaction sites from docking energy landscapes.

21 January 2018

1 reference

21 January 2018

1 reference

A fast method to predict protein interaction sites from sequences

21 January 2018

1 reference

An evolution based classifier for prediction of protein interfaces without using protein structures.

21 January 2018

1 reference

Intramolecular surface contacts contain information about protein-protein interface regions.

21 January 2018

1 reference

Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins

21 January 2018

1 reference

Evolutionary predictions of binding surfaces and interactions.

21 January 2018

1 reference

ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information

21 January 2018

1 reference

Exploiting sequence and structure homologs to identify protein-protein binding sites

21 January 2018

1 reference

Protein interactions and ligand binding: from protein subfamilies to functional specificity

21 January 2018

1 reference

Distinguishing structural and functional restraints in evolution in order to identify interaction sites.

21 January 2018

1 reference

Efficient restraints for protein-protein docking by comparison of observed amino acid substitution patterns with those predicted from local environment.

21 January 2018

1 reference

PRISM: protein-protein interaction prediction by structural matching

21 January 2018

1 reference

Prediction of protein--protein interaction sites in heterocomplexes with neural networks.

21 January 2018

1 reference

Statistical analysis and prediction of protein-protein interfaces

21 January 2018

1 reference

Prediction of solvent accessibility and sites of deleterious mutations from protein sequence.

21 January 2018

1 reference

The crystal structure of the BAR domain from human Bin1/amphiphysin II and its implications for molecular recognition

21 January 2018

1 reference

Identifying interaction motifs in CK2beta--a ubiquitous kinase regulatory subunit.

21 January 2018

1 reference

Structural and functional characterization of binding sites in metallocarboxypeptidases based on Optimal Docking Area analysis.

21 January 2018

1 reference

Recognition and cooperation between the ATP-dependent RNA helicase RhlB and ribonuclease RNase E.

21 January 2018

1 reference

Predicting protein interaction sites: binding hot-spots in protein-protein and protein-ligand interfaces.

21 January 2018

1 reference

A systematic study of low-resolution recognition in protein--protein complexes

21 January 2018

1 reference

Protein-protein association: investigation of factors influencing association rates by Brownian dynamics simulations

21 January 2018

1 reference

The kinetics of protein-protein recognition.

21 January 2018

1 reference

On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5.

21 January 2018

1 reference

Identification of critical contact residues in the NC41 epitope of a subtype N9 influenza virus neuraminidase.

21 January 2018

1 reference

N9 neuraminidase complexes with antibodies NC41 and NC10: empirical free energy calculations capture specificity trends observed with mutant binding data

21 January 2018

1 reference

A hot spot of binding energy in a hormone-receptor interface

21 January 2018

1 reference

Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues.

21 January 2018

1 reference

Anatomy of hot spots in protein interfaces

21 January 2018

1 reference

Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces

21 January 2018

1 reference

Analysis and network representation of hotspots in protein interfaces using minimum cut trees.

21 January 2018

1 reference

Analysis of Hot Region Organization in Hub Proteins

21 January 2018

1 reference

Hot spots--a review of the protein-protein interface determinant amino-acid residues

21 January 2018

1 reference

Unraveling hot spots in binding interfaces: progress and challenges

21 January 2018

1 reference

Reaching for high-hanging fruit in drug discovery at protein-protein interfaces

21 January 2018

1 reference

Rapid mapping of protein functional epitopes by combinatorial alanine scanning

21 January 2018

1 reference

Site-directed ligand discovery

21 January 2018

1 reference

The binding interface database (BID): a compilation of amino acid hot spots in protein interfaces.

21 January 2018

1 reference

HotSprint: database of computational hot spots in protein interfaces

21 January 2018

1 reference

Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations

21 January 2018

1 reference

A simple physical model for binding energy hot spots in protein-protein complexes

21 January 2018

1 reference

Spatial chemical conservation of hot spot interactions in protein-protein complexes

21 January 2018

1 reference

HotPoint: hot spot prediction server for protein interfaces

21 January 2018

1 reference

Identification of hot-spot residues in protein-protein interactions by computational docking

21 January 2018

1 reference

Identification of hot spot residues at protein-protein interface

21 January 2018

1 reference

Protein-protein interaction hotspots carved into sequences

21 January 2018

1 reference

Docking and scoring: applications to drug discovery in the interactomics era.

21 January 2018

1 reference

Computational alanine scanning mutagenesis--an improved methodological approach

21 January 2018

1 reference

Probing the effect of point mutations at protein-protein interfaces with free energy calculations

21 January 2018

1 reference

Binding site detection and druggability index from first principles.

21 January 2018

1 reference

Interaction-site prediction for protein complexes: a critical assessment

21 January 2018

1 reference

Critical assessment of methods of protein structure prediction - Round VIII.

21 January 2018

1 reference

The targets of CAPRI Rounds 13-19.

21 January 2018

1 reference

Docking and scoring protein interactions: CAPRI 2009.

21 January 2018

1 reference

Blind predictions of protein interfaces by docking calculations in CAPRI.

21 January 2018

1 reference

Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening

21 January 2018

1 reference

A computer screening approach to immunoglobulin superfamily structures and interactions: discovery of small non-peptidic CD4 inhibitors as novel immunotherapeutics

21 January 2018

1 reference

Functionality maps of binding sites: a multiple copy simultaneous search method

21 January 2018

1 reference

Experimental and computational mapping of the binding surface of a crystalline protein

21 January 2018

1 reference

The multi-copy simultaneous search methodology: a fundamental tool for structure-based drug design

21 January 2018

1 reference