Volume 14, Issue 6

December 2022

Computational biophysics and structural biology of proteins - A Special Issue in Honor of Prof. Haruki Nakamura's 70th birthday

Issue Editors:

Gautam Basu,
Damien Hall,
Nobutoshi Ito

28 articles in this issue

Computational biophysics and structural biology of proteins—a Special Issue in honor of Prof. Haruki Nakamura’s 70th birthday
Damien Hall
Gautam Basu
Nobutoshi Ito
Editorial 03 January 2023 Pages: 1211 - 1222
Some reflections on a career in science and a note of thanks to the contributors of this Special Issue
Haruki Nakamura
Commentary 20 December 2022 Pages: 1223 - 1226
Dr. Haruki Nakamura, the elephant trainer — understanding life phenomena at multiple scales
Kuniaki Nagayama
Commentary 13 December 2022 Pages: 1227 - 1229
Systems biology of protein network
Mariko Okada
Commentary 13 December 2022 Pages: 1231 - 1232
History of Protein Data Bank Japan: standing at the beginning of the age of structural genomics
Genji Kurisu
Gert-Jan Bekker
Atsushi Nakagawa
Commentary Open access 09 December 2022 Pages: 1233 - 1238
A fortunate period of overlap with Prof. Haruki Nakamura
Damien Hall
Commentary 23 December 2022 Pages: 1239 - 1245
The evolution of structural genomics
Daron M. Standley
Tokuichiro Nakanishi
Kazutaka Katoh
Letter Open access 15 December 2022 Pages: 1247 - 1253
Protein folding problem: enigma, paradox, solution
Alexei V. Finkelstein
Natalya S. Bogatyreva
Sergiy O. Garbuzynskiy
Review 11 October 2022 Pages: 1255 - 1272
Using mechanism similarity to understand enzyme evolution
António J. M. Ribeiro
Ioannis G. Riziotis
Janet M. Thornton
Review Open access 03 December 2022 Pages: 1273 - 1280
Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future
Stephen K. Burley
Helen M. Berman
Christine Zardecki
Review Open access 02 December 2022 Pages: 1281 - 1301
Free energy and kinetic rate calculation via non-equilibrium molecular simulation: application to biomolecules
Shinji Iida
Kameda Tomoshi
Review 29 December 2022 Pages: 1303 - 1314
Non-Ewald methods for evaluating the electrostatic interactions of charge systems: similarity and difference
Ikuo Fukuda
Haruki Nakamura
Review 11 January 2023 Pages: 1315 - 1340
Protein–protein interaction prediction methods: from docking-based to AI-based approaches
Yuko Tsuchiya
Yu Yamamori
Kentaro Tomii
Review Open access 17 December 2022 Pages: 1341 - 1348
Advancing the field of computational drug design using multicanonical molecular dynamics-based dynamic docking
Gert-Jan Bekker
Narutoshi Kamiya
Review 19 November 2022 Pages: 1349 - 1358
Computational modelling of plasticity-led evolution
Eden Tian Hwa Ng
Akira R. Kinjo
Review 17 December 2022 Pages: 1359 - 1367
Quantum chemical studies on hydrogen bonds in helical secondary structures
Yu Takano
Hiroko X. Kondo
Haruki Nakamura
Review Open access 06 January 2023 Pages: 1369 - 1378
Explicit versus implicit consideration of binding partners in protein–protein complex to elucidate intrinsic dynamics
Bhaskar Dasgupta
Sandhya P. Tiwari
Review 17 December 2022 Pages: 1379 - 1392
Recent developments of sequence-based prediction of protein–protein interactions
Yoichi Murakami
Kenji Mizuguchi
Review 24 December 2022 Pages: 1393 - 1411
Protein binding sites for drug design
Janez Konc
Dušanka Janežič
Review 09 December 2022 Pages: 1413 - 1421
Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles
Yoshifumi Fukunishi
Junichi Higo
Kota Kasahara
Review Open access 28 November 2022 Pages: 1423 - 1447
Dynamic structures of intrinsically disordered proteins related to the general transcription factor TFIIH, nucleosomes, and histone chaperones
Masahiko Okuda
Yasuo Tsunaka
Yoshifumi Nishimura
Review 18 November 2022 Pages: 1449 - 1472
Functional dynamics of SARS-CoV-2 3C-like protease as a member of clan PA
Akinori Kidera
Kei Moritsugu
Mitsunori Ikeguchi
Review 02 December 2022 Pages: 1473 - 1485
Enrichment patterns of intrinsic disorder in proteins
Ashwini Patil
Review 19 November 2022 Pages: 1487 - 1493
Biophysical studies of amorphous protein aggregation and in vivo immunogenicity
Yutaka Kuroda
Review 23 November 2022 Pages: 1495 - 1501
Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation
Yasuhiro Matsunaga
Motoshi Kamiya
Yuji Sugita
Review Open access 14 December 2022 Pages: 1503 - 1512
Reflecting on mutational and biophysical analysis of Gaussia princeps Luciferase from a structural perspective: a unique bioluminescent enzyme
Nan Wu
Naohiro Kobayashi
Toshio Yamazaki
Review 14 December 2022 Pages: 1513 - 1520
Structural, functional, and physiological properties of anti-(4-hydroxy-3-nitrophenyl)acetyl antibodies during the course of affinity maturation
Masayuki Oda
Review 20 October 2022 Pages: 1521 - 1526
Structural and functional analysis of actin point mutations leading to nemaline myopathy to elucidate their role in actin function
Anna V. Glyakina
Oxana V. Galzitskaya
Letter 13 December 2022 Pages: 1527 - 1538

Volume 14, Issue 6

Computational biophysics and structural biology of proteins—a Special Issue in honor of Prof. Haruki Nakamura’s 70th birthday

Some reflections on a career in science and a note of thanks to the contributors of this Special Issue

Dr. Haruki Nakamura, the elephant trainer — understanding life phenomena at multiple scales

Systems biology of protein network

History of Protein Data Bank Japan: standing at the beginning of the age of structural genomics

A fortunate period of overlap with Prof. Haruki Nakamura

The evolution of structural genomics

Protein folding problem: enigma, paradox, solution

Using mechanism similarity to understand enzyme evolution

Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future

Free energy and kinetic rate calculation via non-equilibrium molecular simulation: application to biomolecules

Non-Ewald methods for evaluating the electrostatic interactions of charge systems: similarity and difference

Protein–protein interaction prediction methods: from docking-based to AI-based approaches

Advancing the field of computational drug design using multicanonical molecular dynamics-based dynamic docking

Computational modelling of plasticity-led evolution

Quantum chemical studies on hydrogen bonds in helical secondary structures

Explicit versus implicit consideration of binding partners in protein–protein complex to elucidate intrinsic dynamics

Recent developments of sequence-based prediction of protein–protein interactions

Protein binding sites for drug design

Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles

Dynamic structures of intrinsically disordered proteins related to the general transcription factor TFIIH, nucleosomes, and histone chaperones

Functional dynamics of SARS-CoV-2 3C-like protease as a member of clan PA

Enrichment patterns of intrinsic disorder in proteins

Biophysical studies of amorphous protein aggregation and in vivo immunogenicity

Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation

Reflecting on mutational and biophysical analysis of Gaussia princeps Luciferase from a structural perspective: a unique bioluminescent enzyme

Structural, functional, and physiological properties of anti-(4-hydroxy-3-nitrophenyl)acetyl antibodies during the course of affinity maturation

Structural and functional analysis of actin point mutations leading to nemaline myopathy to elucidate their role in actin function

Navigation

Volume 14, Issue 6

Search

Navigation