Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions (Q34083289)

30 July 2017

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions (English)

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protein-protein interaction

30 July 2017

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38

Chaok Seok

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30 July 2017

Mayuko Takeda-Shitaka

45

Mayuko Takeda-Shitaka

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30 July 2017

Krishna Praneeth Kilambi

22

Krishna Praneeth Kilambi

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30 July 2017

69

Shoshana J Wodak

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Nan Zhao

Nan Zhao

28

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Yves Dehouck

Yves Dehouck

13

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Panagiotis L. Kastritis

Panagiotis L Kastritis

6

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Iain H Moal

Iain Moal

14

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Brian G Pierce

Brian G Pierce

52

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Sameer Velankar

Sameer Velankar

67

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Jeffrey J. Gray

Jeffrey J Gray

23

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Dima Kozakov

Dima Kozakov

50

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Sarel J Fleishman

Sarel J Fleishman

2

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Juan Fernández-Recio

Juan Fernandez-Recio

19

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Paul A. Bates

Paul A Bates

5

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Huan-Xiang Zhou

Huan-Xiang Zhou

64

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David Baker

David Baker

70

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Miguel Romero-Durana

Miguel Romero-Durana

15

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Chiara Pallara

Chiara Pallara

17

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Brian Jimenez

Brian Jimenez

18

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Haruki Nakamura

35

Haruki Nakamura

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30 July 2017

27

Daisuke Kihara

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30 July 2017

62

Martin Zacharias

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30 July 2017

68

Joël Janin

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30 July 2017

54

Thom Vreven

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30 July 2017

37

Hahnbeom Park

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30 July 2017

36

Hasup Lee

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30 July 2017

Rocco Moretti

1

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30 July 2017

Rudi Agius

3

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30 July 2017

Mieczyslaw Torchala

4

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30 July 2017

João P G L M Rodrigues

7

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30 July 2017

Mikaël Trellet

8

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30 July 2017

Alexandre M J J Bonvin

9

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30 July 2017

Meng Cui

10

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30 July 2017

Marianne Rooman

11

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30 July 2017

Dimitri Gillis

12

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30 July 2017

Laura Perez-Cano

16

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30 July 2017

Samuel Flores

20

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30 July 2017

Michael Pacella

21

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30 July 2017

Petr Popov

24

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30 July 2017

Sergei Grudinin

25

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30 July 2017

Juan Esquivel-Rodríguez

26

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30 July 2017

Dmitry Korkin

29

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30 July 2017

Xiaolei Zhu

30

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30 July 2017

Omar N A Demerdash

31

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30 July 2017

Julie C Mitchell

32

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30 July 2017

Eiji Kanamori

33

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30 July 2017

Yuko Tsuchiya

34

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30 July 2017

Jamica Sarmiento

39

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30 July 2017

Shide Liang

40

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30 July 2017

Shusuke Teraguchi

41

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30 July 2017

Daron M Standley

42

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30 July 2017

Hiromitsu Shimoyama

43

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30 July 2017

Genki Terashi

44

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30 July 2017

Mitsuo Iwadate

46

1 reference

30 July 2017

Hideaki Umeyama

47

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30 July 2017

Dmitri Beglov

48

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30 July 2017

David R Hall

49

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30 July 2017

Sandor Vajda

51

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30 July 2017

Howook Hwang

53

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30 July 2017

Zhiping Weng

55

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30 July 2017

Yangyu Huang

56

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30 July 2017

Haotian Li

57

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30 July 2017

Xiufeng Yang

58

1 reference

30 July 2017

Xiaofeng Ji

59

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30 July 2017

Shiyong Liu

60

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30 July 2017

Yi Xiao

61

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30 July 2017

Sanbo Qin

63

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30 July 2017

Sheng-You Huang

65

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30 July 2017

Xiaoqin Zou

66

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30 July 2017

language of work or name

English

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publication date

23 August 2013

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30 July 2017

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30 July 2017

81

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30 July 2017

11

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30 July 2017

1980-1987

1 reference

On the binding affinity of macromolecular interactions: daring to ask why proteins interact

30 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

The spatial architecture of protein function and adaptation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

Prediction of protein-protein binding free energies

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

Designing coarse grained-and atom based-potentials for protein-protein docking

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

Protein-protein docking tested in blind predictions: the CAPRI experiment

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

High-resolution mapping of protein sequence-function relationships

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

Protein-protein interaction and quaternary structure

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

Structure-based design of a T-cell receptor leads to nearly 100-fold improvement in binding affinity for pepMHC.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

Comprehensive and quantitative mapping of energy landscapes for protein-protein interactions by rapid combinatorial scanning

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

Protein stability promotes evolvability

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

A new generation of statistical potentials for proteins.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

ROCR: visualizing classifier performance in R

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

Inhibiting protein-protein interactions using designed molecules

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

Prediction of protein-protein interactions: the CAPRI experiment, its evaluation and implications

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

Protein fragment reconstruction using various modeling techniques

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

Small-molecule inhibitors of protein-protein interactions: progressing towards the dream

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

Diversity of protein-protein interactions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

CAPRI: a Critical Assessment of PRedicted Interactions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

How to guarantee optimal stability for most representative structures in the Protein Data Bank.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

Effective energy function for proteins in solution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

Determination of atomic desolvation energies from the structures of crystallized proteins.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct?

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

Energy functions that discriminate X-ray and near native folds from well-constructed decoys

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

Principles of protein-protein interactions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

Amino acid substitution matrices from protein blocks

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4143140

Protein-protein binding affinity prediction on a diverse set of structures

5 July 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24356

An introduction to ROC analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24356

Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24356

A novel high resolution Calpha--Calpha distance dependent force field based on a high quality decoy set.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24356

A physical reference state unifies the structure-derived potential of mean force for protein folding and binding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24356

Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24356

Derivation of protein-specific pair potentials based on weak sequence fragment similarity

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23843247

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PROT.24356

1 reference

30 July 2017

1 reference

30 July 2017

1 reference