Dima Kozakov

Molecular Biology · 2006–2021

A researcher in the Science corpus: 18 papers; trusts 28 researchers and is trusted by 14 researchers here, as inferred from the citation graph.

Subfields

• Molecular Biology — 313 citations into it; #3,455 of 17,773 by trust here, #4,377 by citations
• Materials Chemistry — 156 citations into it
• Computational Theory and Mathematics — 109 citations into it
• Computational Biology & Bioinformatics — 66 citations into it
• Radiology, Nuclear Medicine and Imaging — 41 citations into it; #833 of 3,265 by trust here, #1,376 by citations
• Computational Chemistry & Drug Discovery — 29 citations into it
• Spectroscopy — 21 citations into it

Whom Dima Kozakov trusts overall

Their strongest outbound trust, strongest first, inferred from their citations.

1. Rong Chen
2. Stephen R. Comeau
3. Ryan Brenke
4. Bernard R. Brooks
5. Sandor Vajda
6. S. Parasuraman
7. Marc F. Lensink
8. Joël Janin
9. Junmei Wang
10. Zhiping Weng

Who trusts Dima Kozakov overall

1. Kathryn A. Porter
2. D. Ritchie
3. Sandor Vajda
4. Isak Johansson-Åkhe
5. Israel T. Desta
6. Shengyou Huang
7. David R. Hall
8. Brian G. Pierce
9. Tomer Tsaban
10. Dmitri Beglov

Papers from Dima Kozakov's perspective

Ordered by how strongly the researchers Dima Kozakov trusts endorse each paper. Same corpus, a different order for every researcher.

1. A protein–protein docking benchmark (Proteins: Structure, Function, and Bioinformatics)
2. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques.
3. TM-align: a protein structure alignment algorithm based on the TM-score
4. Docking and scoring protein complexes: CAPRI 3rd Edition
5. Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing
6. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
7. Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS) (Nature Methods)
8. Protein data bank
9. ClusPro: an automated docking and discrimination method for the prediction of protein complexes (Bioinform.)
10. Prediction of protein-protein interactions by docking methods. (Current Opinion in Structural Biology)

Their papers

• Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment (2016) — 130 citations
• Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment (2019) — 104 citations
• Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment (2021) — 103 citations
• High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock (2017) — 144 citations
• PIPER: An FFT‐based protein docking program with pairwise potentials (2006) — 870 citations
• Side-chain Packing Using SE(3)-Transformer (2021) — 7 citations
• Protein–protein docking by fast generalized Fourier transforms on 5D rotational manifolds (2016) — 56 citations
• Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques (2009) — 433 citations
• How Good is Automated Protein Docking? (2013) — 724 citations
• Performance and its limits in rigid body protein-protein docking (2020) — 603 citations
• Allostery in Its Many Disguises: From Theory to Applications (2019) — 322 citations
• What Method to Use for Protein-Protein Docking? (2019) — 88 citations
• New additions to the ClusPro server motivated by CAPRI (2017) — 563 citations
• The ClusPro web server for protein-protein docking (2017) — 2,958 citations
• The FTMap family of web servers for determining and characterizing ligand binding hot spots of proteins (2015) — 562 citations
• Community‐wide evaluation of methods for predicting the effect of mutations on protein–protein interactions (2013) — 102 citations
• Analysis of protein binding sites by computational solvent mapping (2012) — 26 citations
• Application of asymmetric statistical potentials to antibody-protein docking (2012) — 198 citations